Polypeptides Having Endoglucanase Activity and Polynucleotides Encoding Same

ABSTRACT

The present invention relates to isolated polypeptides having endoglucanase activity, catalytic domains, cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains or cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains or cellulose binding domains.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH AND DEVELOPMENT

This invention was made with Government support under CooperativeAgreement DE-FC36-08GO18080 awarded by the Department of Energy. Thegovernment has certain rights in this invention.

REFERENCE TO A SEQUENCE LISTING

This application contains a Sequence Listing in computer readable form,which is incorporated herein by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to polypeptides having endoglucanaseactivity, catalytic domains, and cellulose binding domains, andpolynucleotides encoding the polypeptides, catalytic domains, andcellulose binding domains. The present invention also relates to nucleicacid constructs, vectors, and host cells comprising the polynucleotidesas well as methods of producing and using the polypeptides, catalyticdomains, and cellulose binding domains.

2. Description of the Related Art

Cellulose is a polymer of the simple sugar glucose covalently linked bybeta-1,4-bonds. Many microorganisms produce enzymes that hydrolyzebeta-linked glucans. These enzymes include endoglucanases,cellobiohydrolases, and beta-glucosidases. Endoglucanases digest thecellulose polymer at random locations, opening it to attack bycellobiohydrolases. Cellobiohydrolases sequentially release molecules ofcellobiose from the ends of the cellulose polymer. Cellobiose is awater-soluble beta-1,4-linked dimer of glucose. Beta-glucosidaseshydrolyze cellobiose to glucose.

The conversion of lignocellulosic feedstocks into ethanol has theadvantages of the ready availability of large amounts of feedstock, thedesirability of avoiding burning or land filling the materials, and thecleanliness of the ethanol fuel. Wood, agricultural residues, herbaceouscrops, and municipal solid wastes have been considered as feedstocks forethanol production. These materials primarily consist of cellulose,hemicellulose, and lignin. Once the lignocellulose is converted tofermentable sugars, e.g., glucose, the fermentable sugars are easilyfermented by yeast into ethanol.

The present invention provides polypeptides having endoglucanaseactivity and polynucleotides encoding the polypeptides. The deducedamino acid sequence of the Talaromyces leycettanus gene encoding theP23YSZ GH7 polypeptide having endoglucanase activity shares 74.2%identity (excluding gaps) to the deduced amino acid sequence of apredicted GH7 family protein from Neosartorya fischeri (accession numberSWISSPROT:A1 DKY9) with endoglucanase activity.

SUMMARY OF THE INVENTION

The present invention relates to isolated polypeptides havingendoglucanase activity, selected from the group consisting of:

(a) a polypeptide having at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the mature polypeptide of SEQ ID NO: 2;

(b) a polypeptide encoded by a polynucleotide that hybridizes undermedium-high stringency conditions, high stringency conditions, or veryhigh stringency conditions with (i) the mature polypeptide codingsequence of SEQ ID NO: 1, or (ii) the full-length complement of (i);

(c) a polypeptide encoded by a polynucleotide having at least 75%, atleast 80%, at least 85%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the maturepolypeptide coding sequence of SEQ ID NO: 1;

(d) a variant of the mature polypeptide of SEQ ID NO: 2 comprising asubstitution, deletion, and/or insertion at one or several positions;and (e) a fragment of the polypeptide of (a), (b), (c), or (d) that hasendoglucanase activity.

The present invention also relates to isolated polypeptide comprising acatalytic domain selected from the group consisting of:

(a) a catalytic domain having at least 80% sequence identity to aminoacids 19 to 397 of SEQ ID NO: 2;

(b) a catalytic domain encoded by a polynucleotide that hybridizes underhigh, or very high stringency conditions with (i) nucleotides 55 to 1191of SEQ ID NO: 1, or (ii) the full-length complement of (i);

(c) a catalytic domain encoded by a polynucleotide having at least 80%sequence identity to the catalytic domain of SEQ ID NO: 1;

(d) a variant of amino acids 19 to 397 of SEQ ID NO: 2 comprising asubstitution, deletion, and/or insertion at one or several positions;and

(e) a fragment of the catalytic domain of (a), (b), (c), or (d) that hasendoglucanase activity.

The present invention also relates to an isolated polypeptide comprisinga cellulose binding domain operably linked to a catalytic domain,wherein the binding domain is selected from the roup consisting of:

(a) a cellulose binding domain having at least 80% sequence identity toamino acids 444 to 477 of SEQ ID NO: 2;

(b) a cellulose binding domain encoded by a polynucleotide thathybridizes under high, or very high stringency conditions with (i)nucleotides 1333 to 1431 of SEQ ID NO: 1, or (ii) the full-lengthcomplement of (i);

(c) a cellulose binding domain encoded by a polynucleotide having atleast 80% sequence identity to nucleotides 1333 to 1431 of SEQ ID NO: 1;

(d) a variant of amino acids 444 to 477 of SEQ ID NO: 2 comprising asubstitution, deletion, and/or insertion at one or several positions;and

(e) a fragment of (a), (b), (c), (d) or (e) that has cellulose bindingactivity.

The present invention also relates to isolated polynucleotides encodingthe polypeptides of the present invention; nucleic acid constructs,recombinant expression vectors, and recombinant host cells comprisingthe polynucleotides; and methods of producing the polypeptides.

The present invention also relates to methods for degrading orconverting a cellulosic material, comprising: treating the cellulosicmaterial with an enzyme composition in the presence of a polypeptidehaving endoglucanase activity of the present invention. In one aspect,the method further comprises recovering the degraded or convertedcellulosic material.

The present invention also relates to methods of producing afermentation product, comprising: (a) saccharifying a cellulosicmaterial with an enzyme composition in the presence of a polypeptidehaving endoglucanase activity of the present invention; (b) fermentingthe saccharified cellulosic material with one or more (e.g., several)fermenting microorganisms to produce the fermentation product; and (c)recovering the fermentation product from the fermentation.

The present invention also relates to methods of fermenting a cellulosicmaterial, comprising: fermenting the cellulosic material with one ormore (e.g., several) fermenting microorganisms, wherein the cellulosicmaterial is saccharified with an enzyme composition in the presence of apolypeptide having endoglucanase activity of the present invention. Inone aspect, the fermenting of the cellulosic material produces afermentation product. In another aspect, the method further comprisesrecovering the fermentation product from the fermentation.

The present invention also relates to a polynucleotide encoding a signalpeptide comprising or consisting of amino acids 1 to 18 of SEQ ID NO: 2,which is operably linked to a gene encoding a protein, wherein the geneis foreign to the polynucleotide encoding the signal peptide; nucleicacid constructs, expression vectors, and recombinant host cellscomprising the polynucleotide; and methods of producing a protein.

DEFINITIONS

Allelic variant: The term “allelic variant” means any of two or morealternative forms of a gene occupying the same chromosomal locus.Allelic variation arises naturally through mutation, and may result inpolymorphism within populations. Gene mutations can be silent (no changein the encoded polypeptide) or may encode polypeptides having alteredamino acid sequences. An allelic variant of a polypeptide is apolypeptide encoded by an allelic variant of a gene.

Binding domain: The term “cellulose binding domain” means the region ofan enzyme that mediates binding of the enzyme to amorphous regions of acellulose substrate. The cellulose binding domain (CBD) is typicallyfound either at the N-terminal or at the C-terminal extremity of anendoglucanase. In one embodiment the CBD comprises amino acids 444 to477 of SEQ ID NO: 2.

Catalytic domain: The term “catalytic domain” means the region of anenzyme containing the catalytic machinery of the enzyme. In oneembodiment the catalytic domain comprises amino acids 19 to 397 of SEQID NO: 2.

cDNA: The term “cDNA” means a DNA molecule that can be prepared byreverse transcription from a mature, spliced, mRNA molecule obtainedfrom a eukaryotic or prokaryotic cell. cDNA lacks intron sequences thatmay be present in the corresponding genomic DNA. The initial, primaryRNA transcript is a precursor to mRNA that is processed through a seriesof steps, including splicing, before appearing as mature spliced mRNA.

Coding sequence: The term “coding sequence” means a polynucleotide,which directly specifies the amino acid sequence of a polypeptide. Theboundaries of the coding sequence are generally determined by an openreading frame, which begins with a start codon such as ATG, GTG, or TTGand ends with a stop codon such as TAA, TAG, or TGA. The coding sequencemay be a genomic DNA, cDNA, synthetic DNA, or a combination thereof.

Control sequences: The term “control sequences” means nucleic acidsequences necessary for expression of a polynucleotide encoding a maturepolypeptide of the present invention. Each control sequence may benative (i.e., from the same gene) or foreign (i.e., from a differentgene) to the polynucleotide encoding the polypeptide or native orforeign to each other. Such control sequences include, but are notlimited to, a leader, polyadenylation sequence, propeptide sequence,promoter, signal peptide sequence, and transcription terminator. At aminimum, the control sequences include a promoter, and transcriptionaland translational stop signals. The control sequences may be providedwith linkers for the purpose of introducing specific restriction sitesfacilitating ligation of the control sequences with the coding region ofthe polynucleotide encoding a polypeptide.

Expression: The term “expression” includes any step involved in theproduction of a polypeptide including, but not limited to,transcription, post-transcriptional modification, translation,post-translational modification, and secretion.

Expression vector: The term “expression vector” means a linear orcircular DNA molecule that comprises a polynucleotide encoding apolypeptide and is operably linked to control sequences that provide forits expression.

Fragment: The term “fragment” means a polypeptide or a catalytic domainhaving one or more (e.g., several) amino acids absent from the aminoand/or carboxyl terminus of a mature polypeptide or catalytic domain;wherein the fragment has endoglucanase activity. In one aspect, afragment contains at least 379 amino acid residues (e.g., amino acids 19to 397 of SEQ ID NO: 2).

High stringency conditions: The term “high stringency conditions” meansfor probes of at least 100 nucleotides in length, prehybridization andhybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml shearedand denatured salmon sperm DNA, and 50% formamide, following standardSouthern blotting procedures for 12 to 24 hours. The carrier material isfinally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at65° C.

Host cell: The term “host cell” means any cell type that is susceptibleto transformation, transfection, transduction, or the like with anucleic acid construct or expression vector comprising a polynucleotideof the present invention. The term “host cell” encompasses any progenyof a parent cell that is not identical to the parent cell due tomutations that occur during replication.

Isolated: The term “isolated” means a substance in a form or environmentthat does not occur in nature. Non-limiting examples of isolatedsubstances include (1) any non-naturally occurring substance, (2) anysubstance including, but not limited to, any enzyme, variant, nucleicacid, protein, peptide or cofactor, that is at least partially removedfrom one or more or all of the naturally occurring constituents withwhich it is associated in nature; (3) any substance modified by the handof man relative to that substance found in nature; or (4) any substancemodified by increasing the amount of the substance relative to othercomponents with which it is naturally associated (e.g., multiple copiesof a gene encoding the substance; use of a stronger promoter than thepromoter naturally associated with the gene encoding the substance). Anisolated substance may be present in a fermentation broth sample.

Low stringency conditions: The term “low stringency conditions” meansfor probes of at least 100 nucleotides in length, prehybridization andhybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml shearedand denatured salmon sperm DNA, and 25% formamide, following standardSouthern blotting procedures for 12 to 24 hours. The carrier material isfinally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at50° C.

Mature polypeptide: The term “mature polypeptide” means a polypeptide inits final form following translation and any post-translationalmodifications, such as N-terminal processing, C-terminal truncation,glycosylation, phosphorylation, etc. In one aspect, the maturepolypeptide is amino acids 19 to 477 of SEQ ID NO: 2 based on theSignalP (Nielsen et al., 1997, Protein Engineering 10:1-6) that predictsamino acids 1 to 18 of SEQ ID NO: 2 are a signal peptide. It is known inthe art that a host cell may produce a mixture of two of more differentmature polypeptides (i.e., with a different C-terminal and/or N-terminalamino acid) expressed by the same polynucleotide.

Mature polypeptide coding sequence: The term “mature polypeptide codingsequence” means a polynucleotide that encodes a mature polypeptidehaving endoglucanase activity. In one aspect, the mature polypeptidecoding sequence (including the stop codon) is nucleotides 55 to 1434 ofSEQ ID NO: 1 based on the SignalP (Nielsen et al., 1997, supra) thatpredicts nucleotides 1 to 54 of SEQ ID NO: 1 encode a signal peptide.

Medium stringency conditions: The term “medium stringency conditions”means for probes of at least 100 nucleotides in length, prehybridizationand hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/mlsheared and denatured salmon sperm DNA, and 35% formamide, followingstandard Southern blotting procedures for 12 to 24 hours. The carriermaterial is finally washed three times each for 15 minutes using 2×SSC,0.2% SDS at 55° C.

Medium-high stringency conditions: The term “medium-high stringencyconditions” means for probes of at least 100 nucleotides in length,prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200micrograms/ml sheared and denatured salmon sperm DNA, and either 35%formamide, following standard Southern blotting procedures for 12 to 24hours. The carrier material is finally washed three times each for 15minutes using 2×SSC, 0.2% SDS at 60° C.

Nucleic acid construct: The term “nucleic acid construct” means anucleic acid molecule, either single- or double-stranded, which isisolated from a naturally occurring gene or is modified to containsegments of nucleic acids in a manner that would not otherwise exist innature or which is synthetic, which comprises one or more controlsequences.

Operably linked: The term “operably linked” means a configuration inwhich a control sequence is placed at an appropriate position relativeto the coding sequence of a polynucleotide such that the controlsequence directs expression of the coding sequence.

Sequence identity: The relatedness between two amino acid sequences orbetween two nucleotide sequences is described by the parameter “sequenceidentity”. For purposes of the present invention, the sequence identitybetween two amino acid sequences is determined using theNeedleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol. Biol.48: 443-453) as implemented in the Needle program of the EMBOSS package(EMBOSS: The European Molecular Biology Open Software Suite, Rice etal., 2000, Trends Genet. 16: 276-277), preferably version 5.0.0 orlater. The parameters used are gap open penalty of 10, gap extensionpenalty of 0.5, and the EBLOSUM62 (EMBOSS version of BLOSUM62)substitution matrix. The output of Needle labeled “longest identity”(obtained using the—nobrief option) is used as the percent identity andis calculated as follows:

(Identical Residues×100)/(Length of Alignment−Total Number of Gaps inAlignment)

For purposes of the present invention, the sequence identity between twodeoxyribonucleotide sequences is determined using the Needleman-Wunschalgorithm (Needleman and Wunsch, 1970, supra) as implemented in theNeedle program of the EMBOSS package (EMBOSS: The European MolecularBiology Open Software Suite, Rice et al., 2000, supra), preferablyversion 5.0.0 or later. The parameters used are gap open penalty of 10,gap extension penalty of 0.5, and the EDNAFULL (EMBOSS version of NCBINUC4.4) substitution matrix. The output of Needle labeled “longestidentity” (obtained using the—nobrief option) is used as the percentidentity and is calculated as follows:

(Identical Deoxyribonucleotides×100)/(Length of Alignment−Total Numberof Gaps in Alignment)

Subsequence: The term “subsequence” means a polynucleotide having one ormore (e.g., several) nucleotides absent from the 5′ and/or 3′ end of amature polypeptide coding sequence; wherein the subsequence encodes afragment having endoglucanase activity. In one aspect, a subsequencecontains at least 1377 nucleotides (e.g., nucleotides 55 to 1431 of SEQID NO: 1).

Variant: The term “variant” means a polypeptide having endoglucanaseactivity comprising an alteration, i.e., a substitution, insertion,and/or deletion, at one or more (e.g., several) positions. Asubstitution means replacement of the amino acid occupying a positionwith a different amino acid; a deletion means removal of the amino acidoccupying a position; and an insertion means adding an amino acidadjacent to and immediately following the amino acid occupying aposition.

Very high stringency conditions: The term “very high stringencyconditions” means for probes of at least 100 nucleotides in length,prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200micrograms/ml sheared and denatured salmon sperm DNA, and 50% formamide,following standard Southern blotting procedures for 12 to 24 hours. Thecarrier material is finally washed three times each for 15 minutes using2×SSC, 0.2% SDS at 70° C.

Very low stringency conditions: The term “very low stringencyconditions” means for probes of at least 100 nucleotides in length,prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200micrograms/ml sheared and denatured salmon sperm DNA, and 25% formamide,following standard Southern blotting procedures for 12 to 24 hours. Thecarrier material is finally washed three times each for 15 minutes using2×SSC, 0.2% SDS at 45° C.

Cellulolytic activity: The term “cellulolytic activity” means abiological activity that hydrolyzes a cellulosic material. The two basicapproaches for measuring cellulolytic activity include: (1) measuringthe total cellulolytic activity, and (2) measuring the individualcellulolytic activities (endoglucanases, cellobiohydrolases, andbeta-glucosidases) as reviewed in Zhang et al., 2006, Outlook forcellulase improvement: Screening and selection strategies, BiotechnologyAdvances 24: 452-481. Total cellulolytic activity is usually measuredusing insoluble substrates, including Whatman NQ1 filter paper,microcrystalline cellulose, bacterial cellulose, algal cellulose,cotton, pretreated lignocellulose, etc. The most common totalcellulolytic activity assay is the filter paper assay using Whatman NQ1filter paper as the substrate. The assay was established by theInternational Union of Pure and Applied Chemistry (IUPAC) (Ghose, 1987,Measurement of cellulase activities, Pure Appl. Chem. 59: 257-68).

For purposes of the present invention, cellulolytic activity isdetermined by measuring the increase in hydrolysis of a cellulosicmaterial by cellulolytic enzyme(s) under the following conditions: 1-20mg of cellulolytic protein/g of cellulose in PCS for 3-7 days at 50-65°C. compared to a control hydrolysis without addition of cellulolyticprotein. Typical conditions are 1 ml reactions, washed or unwashed PCS,5% insoluble solids, 50 mM sodium acetate pH 5, 1 mM MnSO₄, 50-65° C.,72 hours, sugar analysis by AMINEX® HPX-87H column (Bio-RadLaboratories, Inc., Hercules, Calif., USA).

Endoglucanase: The term “endoglucanase” means anendo-1,4-(1,3;1,4)-beta-D-glucan 4-glucanohydrolase (E.C. 3.2.1.4),which catalyses endohydrolysis of 1,4-beta-D-glycosidic linkages incellulose, cellulose derivatives (such as carboxymethyl cellulose andhydroxyethyl cellulose), lichenin, beta-1,4 bonds in mixed beta-1,3glucans such as cereal beta-D-glucans or xyloglucans, and other plantmaterial containing cellulosic components. Endoglucanase activity can bedetermined by measuring reduction in substrate viscosity or increase inreducing ends determined by a reducing sugar assay (Zhang et al., 2006,Biotechnology Advances 24: 452-481). For purposes of the presentinvention, endoglucanase activity is determined using carboxymethylcellulose (CMC) as substrate according to the procedure of Ghose, 1987,Pure and Appl. Chem. 59: 257-268, at pH 5, 40° C. The assay described inExample 8 can be used to measure endoglucanase activity.

The polypeptides of the present invention have at least 20%, e.g., atleast 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95%, and at least 100% of the endoglucanase activityof the mature polypeptide of SEQ ID NO: 2.

Cellobiohydrolase: The term “cellobiohydrolase” means a1,4-beta-D-glucan cellobiohydrolase (E.C. 3.2.1.91), which catalyzes thehydrolysis of 1,4-beta-D-glucosidic linkages in cellulose,cellooligosaccharides, or any beta-1,4-linked glucose containingpolymer, releasing cellobiose from the reducing or non-reducing ends ofthe chain (Teeri, 1997, Crystalline cellulose 5 degradation: New insightinto the function of cellobiohydrolases, Trends in Biotechnology 15:160-167; Teeri et al., 1998, Trichoderma reesei cellobiohydrolases: whyso efficient on crystalline cellulose?, Biochem. Soc. Trans. 26:173-178). For purposes of the present invention, cellobiohydrolaseactivity is determined using a fluorescent disaccharide derivative4-methylumbelliferyl-β-D-lactoside according to the procedures describedby van Tilbeurgh et al., 101982, FEBS Letters 149: 152-156 and vanTilbeurgh and Claeyssens, 1985, FEBS Letters 187: 283-288, at pH 5, 40°C.

Beta-glucosidase: The term “beta-glucosidase” means a beta-D-glucosideglucohydrolase (E.C. 3.2.1.21), which catalyzes the hydrolysis ofterminal non-reducing beta-D-glucose residues with the release ofbeta-D-glucose. For purposes of the present invention, beta-glucosidaseactivity is determined according to the basic procedure described byVenturi et al., 2002, Extracellular beta-D-glucosidase from Chaetomiumthermophilum var. coprophilum: production, purification and somebiochemical properties, J. Basic Microbiol. 42: 55-66. One unit ofbeta-glucosidase is defined as 1.0 pmole of p-nitrophenol produced perminute at 40° C., pH 5 from 1 mM p-nitrophenyl-beta-D-glucopyranoside assubstrate in 100 mM sodium citrate containing 0.01% TWEEN® 20.

Cellulolytic enhancing activity: The term “cellulolytic enhancingactivity” means a biological activity catalyzed by a GH61 polypeptidethat enhances the hydrolysis of a cellulosic material by enzyme havingcellulolytic activity. For purposes of the present invention,cellulolytic enhancing activity is determined by measuring the increasein reducing sugars or the increase of the total of cellobiose andglucose from the hydrolysis of a cellulosic material by cellulolyticenzyme under the following conditions: 1-50 mg of total protein/g ofcellulose in PCS, wherein total protein is comprised of 50-99.5% w/wcellulolytic protein and 0.5-50% w/w protein of a GH61 polypeptidehaving cellulolytic enhancing activity for 1-7 day at 50-65° C. comparedto a control hydrolysis with equal total protein loading withoutcellulolytic enhancing activity (1-50 mg of cellulolytic protein/g ofcellulose in PCS). In a preferred aspect, a mixture of CELLUCLAST® 1.5L(Novozymes A/S, Bagsvrd, Denmark) in the presence of 3% of total proteinweight Aspergillus oryzae beta-glucosidase (recombinantly produced inAspergillus oryzae according to WO 02/095014) or 3% of total proteinweight Aspergillus fumigatus beta-glucosidase (recombinantly produced inAspergillus oryzae as described in WO 2002/095014) of cellulase proteinloading is used as the source of the cellulolytic activity.

The GH61 polypeptides having cellulolytic enhancing activity enhance thehydrolysis of a cellulosic material catalyzed by enzyme havingcellulolytic activity by reducing the amount of cellulolytic enzymerequired to reach the same degree of hydrolysis preferably at least1.01-fold, more preferably at least 1.05-fold, more preferably at least1.10-fold, more preferably at least 1.25-fold, more preferably at least1.5-fold, more preferably at least 2-fold, more preferably at least3-Fold, more preferably at least 4-fold, more preferably at least5-fold, even more preferably at least 10-fold, and most preferably atleast 20-fold.

Family 61 glycoside hydrolase: The term “Family 61 glycoside hydrolase”or “Family GH61” or “GH61” means a polypeptide falling into theglycoside hydrolase Family 61 according to Henrissat, 1991, Aclassification of glycosyl hydrolases based on amino-acid sequencesimilarities, Biochem. J. 280: 309-316, and Henrissat and Bairoch, 1996,Updating the sequence-based classification of glycosyl hydrolases,Biochem. J. 316: 695-696.

Xylan degrading activity: The terms “xylan degrading activity” or“xylanolytic activity” mean a biological activity that hydrolyzesxylan-containing material. The two basic approaches for measuringxylanolytic activity include: (1) measuring the total xylanolyticactivity, and (2) measuring the individual xylanolytic activities(endoxylanases, beta-xylosidases, arabinofuranosidases,alpha-glucuronidases, acetylxylan esterases, feruloyl esterases, andalpha-glucuronyl esterases). Recent progress in assays of xylanolyticenzymes was summarized in several publications including Biely andPuchard, Recent progress in the assays of xylanolytic enzymes, 2006,Journal of the Science of Food and Agriculture 86(11): 1636-1647;Spanikova and Biely, 2006, Glucuronoyl esterase—Novel carbohydrateesterase produced by Schizophyllum commune, FEBS Letters 580(19):4597-4601; Herrmann et al., 1997, The beta-D-xylosidase of Trichodermareesei is a multifunctional beta-D-xylan xylohydrolase, BiochemicalJournal 321: 375-381.

Total xylan degrading activity can be measured by determining thereducing sugars formed from various types of xylan, including, forexample, oat spelt, beechwood, and larchwood xylans, or by photometricdetermination of dyed xylan fragments released from various covalentlydyed xylans. The most common total xylanolytic activity assay is basedon production of reducing sugars from polymeric 4-O-methylglucuronoxylan as described in Bailey et al., 1992, Interlaboratorytesting of methods for assay of xylanase activity, Journal ofBiotechnology 23(3): 257-270.

For purposes of the present invention, xylan degrading activity isdetermined by measuring the increase in hydrolysis of birchwood xylan(Sigma Chemical Co., Inc., St. Louis, Mo., USA) by xylan-degradingenzyme(s) under the following typical conditions: 1 ml reactions, 5mg/ml substrate (total solids), 5 mg of xylanolytic protein/g ofsubstrate, 50 mM sodium acetate pH 5, 50° C., 24 hours, sugar analysisusing p-hydroxybenzoic acid hydrazide (PHBAH) assay as described byLever, 1972, A new reaction for colorimetric determination ofcarbohydrates, Anal. Biochem 47: 273-279.

Xylanase: The term “xylanase” means a 1,4-beta-D-xylan-xylohydrolase(E.C. 3.2.1.8) that catalyzes the endo-hydrolysis of1,4-beta-D-xylosidic linkages in xylans. For purposes of the presentinvention, xylanase activity is determined using birchwood xylan assubstrate. One unit of xylanase is defined as 1.0 mmole of reducingsugar (measured in glucose equivalents as described by Lever, 1972, Anew reaction for colorimetric determination of carbohydrates, Anal.Biochem 47: 273-279) produced per minute during the initial period ofhydrolysis at 50° C., pH 5 from 2 g of birchwood xylan per liter assubstrate in 50 mM sodium acetate containing 0.01% TWEEN® 20.

Beta-xylosidase: The term “beta-xylosidase” means a beta-D-xylosidexylohydrolase (E.C. 3.2.1.37) that catalyzes the exo-hydrolysis of shortbeta (44)-xylooligosaccharides, to remove successive D-xylose residuesfrom the non-reducing termini. For purposes of the present invention,one unit of beta-xylosidase is defined as 1.0 pmole of p-nitrophenolproduced per minute at 40° C., pH 5 from 1 mMp-nitrophenyl-beta-D-xyloside as substrate in 100 mM sodium citratecontaining 0.01% TWEEN® 20.

Acetylxylan esterase: The term “acetylxylan esterase” means acarboxylesterase (EC 3.1.1.72) that catalyses the hydrolysis of acetylgroups from polymeric xylan, acetylated xylose, acetylated glucose,alpha-napthyl acetate, and p-nitrophenyl acetate. For purposes of thepresent invention, acetylxylan esterase activity is determined using 0.5mM p-nitrophenylacetate as substrate in 50 mM sodium acetate pH 5.0containing 0.01% TWEEN™ 20. One unit of acetylxylan esterase is definedas the amount of enzyme capable of releasing 1 μmole of p-nitrophenolateanion per minute at pH 5, 25° C.

Feruloyl esterase: The term “feruloyl esterase” means a4-hydroxy-3-methoxycinnamoyl-sugar hydrolase (EC 3.1.1.73) thatcatalyzes the hydrolysis of the 4-hydroxy-3-methoxycinnamoyl (feruloyl)group from an esterified sugar, which is usually arabinose in “natural”substrates, to produce ferulate (4-hydroxy-3-methoxycinnamate). Feruloylesterase is also known as ferulic acid esterase, hydroxycinnamoylesterase, FAE-III, cinnamoyl ester hydrolase, FAEA, cinnAE, FAE-I, orFAE-II. For purposes of the present invention, feruloyl esteraseactivity is determined using 0.5 mM p-nitrophenylferulate as substratein 50 mM sodium acetate pH 5.0. One unit of feruloyl esterase equals theamount of enzyme capable of releasing 1 pmole of p-nitrophenolate anionper minute at pH 5, 25° C.

Alpha-glucuronidase: The term “alpha-glucuronidase” means analpha-D-glucosiduronate glucuronohydrolase (EC 3.2.1.139) that catalyzesthe hydrolysis of an alpha-D-glucuronoside to D-glucuronate and analcohol. For purposes of the present invention, alpha-glucuronidaseactivity is determined according to de Vries, 1998, J. Bacteriol. 180:243-249. One unit of alpha-glucuronidase equals the amount of enzymecapable of releasing 1 pmole of glucuronic or 4-O-methylglucuronic acidper minute at pH 5, 40° C.

Alpha-L-arabinofuranosidase: The term “alpha-L-arabinofuranosidase”means an alpha-L-arabinofuranoside arabinofuranohydrolase (EC 3.2.1.55)that catalyzes the hydrolysis of terminal non-reducingalpha-L-arabinofuranoside residues in alpha-L-arabinosides. The enzymeacts on alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)-and/or (1,5)-linkages, arabinoxylans, and arabinogalactans.Alpha-L-arabinofuranosidase is also known as arabinosidase,alpha-arabinosidase, alpha-L-arabinosidase, alpha-arabinofuranosidase,polysaccharide alpha-L-arabinofuranosidase, alpha-L-arabinofuranosidehydrolase, L-arabinosidase, or alpha-L-arabinanase. For purposes of thepresent invention, alpha-L-arabinofuranosidase activity is determinedusing 5 mg of medium viscosity wheat arabinoxylan (MegazymeInternational Ireland, Ltd., Bray, Co. Wicklow, Ireland) per ml of 100mM sodium acetate pH 5 in a total volume of 200 μl for 30 minutes at 40°C. followed by arabinose analysis by AMINEX® HPX-87H columnchromatography (Bio-Rad Laboratories, Inc., Hercules, Calif., USA).

Cellulosic material: The cellulosic material can be any materialcontaining cellulose. The predominant polysaccharide in the primary cellwall of biomass is cellulose, the second most abundant is hemicellulose,and the third is pectin. The secondary cell wall, produced after thecell has stopped growing, also contains polysaccharides and isstrengthened by polymeric lignin covalently cross-linked tohemicellulose. Cellulose is a homopolymer of anhydrocellobiose and thusa linear beta-(1-4)-D-glucan, while hemicelluloses include a variety ofcompounds, such as xylans, xyloglucans, arabinoxylans, and mannans incomplex branched structures with a spectrum of substituents. Althoughgenerally polymorphous, cellulose is found in plant tissue primarily asan insoluble crystalline matrix of parallel glucan chains.Hemicelluloses usually hydrogen bond to cellulose, as well as to otherhemicelluloses, which help stabilize the cell wall matrix.

Cellulose is generally found, for example, in the stems, leaves, hulls,husks, and cobs of plants or leaves, branches, and wood of trees. Thecellulosic material can be, but is not limited to, herbaceous material,agricultural residue, forestry residue, municipal solid waste, wastepaper, and pulp and paper mill residue (see, for example, Wiselogel etal., 1995, in Handbook on Bioethanol (Charles E. Wyman, editor), pp.105-118, Taylor & Francis, Washington D.C.; Wyman, 1994, BioresourceTechnology 50: 3-16; Lynd, 1990, Applied Biochemistry and Biotechnology24/25: 695-719; Mosier et al., 1999, Recent Progress in Bioconversion ofLignocellulosics, in Advances in Biochemical Engineering/Biotechnology,T. Scheper, managing editor, Volume 65, pp. 23-40, Springer-Verlag, NewYork). It is understood herein that the cellulose may be in the form oflignocellulose, a plant cell wall material containing lignin, cellulose,and hemicellulose in a mixed matrix. In a preferred aspect, thecellulosic material is lignocellulose.

In one aspect, the cellulosic material is herbaceous material. Inanother aspect, the cellulosic material is agricultural residue. Inanother aspect, the cellulosic material is forestry residue. In anotheraspect, the cellulosic material is municipal solid waste. In anotheraspect, the cellulosic material is waste paper. In another aspect, thecellulosic material is pulp and paper mill residue.

In another aspect, the cellulosic material is corn stover. In anotheraspect, the cellulosic material is corn fiber. In another aspect, thecellulosic material is corn cob. In another aspect, the cellulosicmaterial is orange peel. In another aspect, the cellulosic material isrice straw. In another aspect, the cellulosic material is wheat straw.In another aspect, the cellulosic material is switch grass. In anotheraspect, the cellulosic material is miscanthus. In another aspect, thecellulosic material is bagasse.

In another aspect, the cellulosic material is microcrystallinecellulose. In another aspect, the cellulosic material is bacterialcellulose. In another aspect, the cellulosic material is algalcellulose. In another aspect, the cellulosic material is cotton linter.In another aspect, the cellulosic material is amorphous phosphoric-acidtreated cellulose. In another aspect, the cellulosic material is filterpaper.

The cellulosic material may be used as is or may be subjected topretreatment, using conventional methods known in the art, as describedherein. In a preferred aspect, the cellulosic material is pretreated.

Pretreated corn stover: The term “PCS” or “Pretreated Corn Stover” meansa cellulosic material derived from corn stover by treatment with heatand dilute sulfuric acid.

Xylan-containing material: The term “xylan-containing material” meansany material comprising a plant cell wall polysaccharide containing abackbone of beta-(1-4)-linked xylose residues. Xylans of terrestrialplants are heteropolymers possessing a beta-(1-4)-D-xylopyranosebackbone, which is branched by short carbohydrate chains. They compriseD-glucuronic acid or its 4-O-methyl ether, L-arabinose, and/or variousoligosaccharides, composed of D-xylose, L-arabinose, D- or L-galactose,and D-glucose. Xylan-type polysaccharides can be divided into homoxylansand heteroxylans, which include glucuronoxylans,(arabino)glucuronoxylans, (glucurono)arabinoxylans, arabinoxylans, andcomplex heteroxylans. See, for example, Ebringerova et al., 2005, Adv.Polym. Sci. 186: 1-67.

In the methods of the present invention, any material containing xylanmay be used. In a preferred aspect, the xylan-containing material islignocellulose.

DETAILED DESCRIPTION OF THE INVENTION Polypeptides Having EndoglucanaseActivity

In an embodiment, the present invention relates to isolated polypeptideshaving a sequence identity to the mature polypeptide of SEQ ID NO: 2 ofat least 75%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100%, which have endoglucanaseactivity. In one aspect, the polypeptides differ by no more than 10amino acids, e.g., 1, 2, 3, 4, 5, 6, 7, 8, or 9, from the maturepolypeptide of SEQ ID NO: 2.

The polypeptides of the present invention have at least 20%, e.g., atleast 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95%, and at least 100% of the endoglucanase activityof the mature polypeptide of SEQ ID NO: 2.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 2 or an allelic variantthereof; or is a fragment thereof having endoglucanase activity. Inanother aspect, the polypeptide comprises or consists of the maturepolypeptide of SEQ ID NO: 2. In another aspect, the polypeptidecomprises or consists of amino acids 19 to 477 of SEQ ID NO: 2.

In another embodiment, the present invention relates to an isolatedpolypeptide having endoglucanase activity encoded by a polynucleotidethat hybridizes under medium-high stringency conditions, high stringencyconditions, or very high stringency conditions with (i) the maturepolypeptide coding sequence of SEQ ID NO: 1, or (ii) the full-lengthcomplement of (i) (Sambrook et al., 1989, Molecular Cloning, ALaboratory Manual, 2d edition, Cold Spring Harbor, N.Y.).

The polynucleotide of SEQ ID NO: 1 or a subsequence thereof, as well asthe polypeptide of SEQ ID NO: 2 or a fragment thereof, may be used todesign nucleic acid probes to identify and clone DNA encodingpolypeptides having endoglucanase activity from strains of differentgenera or species according to methods well known in the art. Inparticular, such probes can be used for hybridization with the genomicDNA or cDNA of a cell of interest, following standard Southern blottingprocedures, in order to identify and isolate the corresponding genetherein. Such probes can be considerably shorter than the entiresequence, but should be at least 15, e.g., at least 25, at least 35, orat least 70 nucleotides in length. Preferably, the nucleic acid probe isat least 100 nucleotides in length, e.g., at least 200 nucleotides, atleast 300 nucleotides, at least 400 nucleotides, at least 500nucleotides, at least 600 nucleotides, at least 700 nucleotides, atleast 800 nucleotides, or at least 900 nucleotides in length. Both DNAand RNA probes can be used. The probes are typically labeled fordetecting the corresponding gene (for example, with ³²P, ³H, ³⁵S,biotin, or avidin). Such probes are encompassed by the presentinvention.

A genomic DNA or cDNA library prepared from such other strains may bescreened for DNA that hybridizes with the probes described above andencodes a polypeptide having endoglucanase activity. Genomic or otherDNA from such other strains may be separated by agarose orpolyacrylamide gel electrophoresis, or other separation techniques. DNAfrom the libraries or the separated DNA may be transferred to andimmobilized on nitrocellulose or other suitable carrier material. Inorder to identify a clone or DNA that hybridizes with SEQ ID NO: 1 or asubsequence thereof, the carrier material is used in a Southern blot.

For purposes of the present invention, hybridization indicates that thepolynucleotide hybridizes to a labeled nucleic acid probe correspondingto (i) SEQ ID NO: 1; (ii) the mature polypeptide coding sequence of SEQID NO: 1; (iii) the full-length complement thereof; or (iv) asubsequence thereof; under very low to very high stringency conditions.Molecules to which the nucleic acid probe hybridizes under theseconditions can be detected using, for example, X-ray film or any otherdetection means known in the art.

In one aspect, the nucleic acid probe is nucleotides 1 to 1434,nucleotides 55 to 1434, or nucleotides 55 to 1191 of SEQ ID NO: 1. Inanother aspect, the nucleic acid probe is a polynucleotide that encodesthe polypeptide of SEQ ID NO: 2; the mature polypeptide thereof; or afragment thereof. In another aspect, the nucleic acid probe is SEQ IDNO: 1.

In another embodiment, the present invention relates to an isolatedpolypeptide having endoglucanase activity encoded by a polynucleotidehaving a sequence identity to the mature polypeptide coding sequence ofSEQ ID NO: 1 at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100%.

In another embodiment, the present invention relates to variants of themature polypeptide of SEQ ID NO: 2 comprising a substitution, deletion,and/or insertion at one or more (e.g., several) positions. In anembodiment, the number of amino acid substitutions, deletions and/orinsertions introduced into the mature polypeptide of SEQ ID NO: 2 is notmore than 10, e.g., 1, 2, 3, 4, 5, 6, 7, 8 or 9. The amino acid changesmay be of a minor nature, that is conservative amino acid substitutionsor insertions that do not significantly affect the folding and/oractivity of the protein; small deletions, typically of 1-30 amino acids;small amino- or carboxyl-terminal extensions, such as an amino-terminalmethionine residue; a small linker peptide of up to 20-25 residues; or asmall extension that facilitates purification by changing net charge oranother function, such as a poly-histidine tract, an antigenic epitopeor a binding domain.

Examples of conservative substitutions are within the groups of basicamino acids (arginine, lysine and histidine), acidic amino acids(glutamic acid and aspartic acid), polar amino acids (glutamine andasparagine), hydrophobic amino acids (leucine, isoleucine and valine),aromatic amino acids (phenylalanine, tryptophan and tyrosine), and smallamino acids (glycine, alanine, serine, threonine and methionine). Aminoacid substitutions that do not generally alter specific activity areknown in the art and are described, for example, by H. Neurath and R. L.Hill, 1979, In, The Proteins, Academic Press, New York. Commonsubstitutions are Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser, Ala/Gly, Ala/Thr,Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/Ile,Leu/Val, Ala/Glu, and Asp/Gly.

Alternatively, the amino acid changes are of such a nature that thephysico-chemical properties of the polypeptides are altered. Forexample, amino acid changes may improve the thermal stability of thepolypeptide, alter the substrate specificity, change the pH optimum, andthe like.

Essential amino acids in a polypeptide can be identified according toprocedures known in the art, such as site-directed mutagenesis oralanine-scanning mutagenesis (Cunningham and Wells, 1989, Science 244:1081-1085). In the latter technique, single alanine mutations areintroduced at every residue in the molecule, and the resultant mutantmolecules are tested for endoglucanase activity to identify amino acidresidues that are critical to the activity of the molecule. See also,Hilton et al., 1996, J. Biol. Chem. 271: 4699-4708. The active site ofthe enzyme or other biological interaction can also be determined byphysical analysis of structure, as determined by such techniques asnuclear magnetic resonance, crystallography, electron diffraction, orphotoaffinity labeling, in conjunction with mutation of putative contactsite amino acids. See, for example, de Vos et al., 1992, Science 255:306-312; Smith et al., 1992, J. Mol. Biol. 224: 899-904; Wlodaver etal., 1992, FEBS Lett. 309: 59-64. The identity of essential amino acidscan also be inferred from an alignment with a related polypeptide.

Single or multiple amino acid substitutions, deletions, and/orinsertions can be made and tested using known methods of mutagenesis,recombination, and/or shuffling, followed by a relevant screeningprocedure, such as those disclosed by Reidhaar-Olson and Sauer, 1988,Science 241: 53-57; Bowie and Sauer, 1989, Proc. Natl. Acad. Sci. USA86: 2152-2156; WO 95/17413; or WO 95/22625. Other methods that can beused include error-prone PCR, phage display (e.g., Lowman et al., 1991,Biochemistry 30: 10832-10837; U.S. Pat. No. 5,223,409; WO 92/06204), andregion-directed mutagenesis (Derbyshire et al., 1986, Gene 46: 145; Neret al., 1988, DNA 7: 127).

Mutagenesis/shuffling methods can be combined with high-throughput,automated screening methods to detect activity of cloned, mutagenizedpolypeptides expressed by host cells (Ness et al., 1999, NatureBiotechnology 17: 893-896). Mutagenized DNA molecules that encode activepolypeptides can be recovered from the host cells and rapidly sequencedusing standard methods in the art. These methods allow the rapiddetermination of the importance of individual amino acid residues in apolypeptide.

The polypeptide may be a hybrid polypeptide in which a region of onepolypeptide is fused at the N-terminus or the C-terminus of a region ofanother polypeptide.

The polypeptide may be a fusion polypeptide or cleavable fusionpolypeptide in which another polypeptide is fused at the N-terminus orthe C-terminus of the polypeptide of the present invention. A fusionpolypeptide is produced by fusing a polynucleotide encoding anotherpolypeptide to a polynucleotide of the present invention. Techniques forproducing fusion polypeptides are known in the art, and include ligatingthe coding sequences encoding the polypeptides so that they are in frameand that expression of the fusion polypeptide is under control of thesame promoter(s) and terminator. Fusion polypeptides may also beconstructed using intein technology in which fusion polypeptides arecreated post-translationally (Cooper et al., 1993, EMBO J. 12:2575-2583; Dawson et al., 1994, Science 266: 776-779).

A fusion polypeptide can further comprise a cleavage site between thetwo polypeptides. Upon secretion of the fusion protein, the site iscleaved releasing the two polypeptides. Examples of cleavage sitesinclude, but are not limited to, the sites disclosed in Martin et al.,2003, J. Ind. Microbiol. Biotechnol. 3: 568-576; Svetina et al., 2000,J. Biotechnol. 76: 245-251; Rasmussen-Wilson et al., 1997, Appl.Environ. Microbiol. 63: 3488-3493; Ward et al., 1995, Biotechnology 13:498-503; and Contreras et al., 1991, Biotechnology 9: 378-381; Eaton etal., 1986, Biochemistry 25: 505-512; Collins-Racie et al., 1995,Biotechnology 13: 982-987; Carter et al., 1989, Proteins: Structure,Function, and Genetics 6: 240-248; and Stevens, 2003, Drug DiscoveryWorld 4: 35-48.

Sources of Polypeptides Having Endoglucanase Activity

A polypeptide having endoglucanase activity of the present invention maybe obtained from a fungus. For purposes of the present invention, theterm “obtained from” as used herein in connection with a given sourceshall mean that the polypeptide encoded by a polynucleotide is producedby the source or by a strain in which the polynucleotide from the sourcehas been inserted. In one aspect, the polypeptide obtained from a givensource is secreted extracellularly.

The polypeptide may be a fungal polypeptide. For example, thepolypeptide may be a filamentous fungal polypeptide such as aTalaromyces polypeptide.

In another aspect, the polypeptide is a Talaromyces polypeptide, e.g., apolypeptide obtained from Talaromyces leycettanus. E.g. obtained fromstrain CBS398.68.

It will be understood that for the aforementioned species, the inventionencompasses both the perfect and imperfect states, and other taxonomicequivalents, e.g., anamorphs, regardless of the species name by whichthey are known. Those skilled in the art will readily recognize theidentity of appropriate equivalents.

Strains of these species are readily accessible to the public in anumber of culture collections, such as the American Type CultureCollection (ATCC), Deutsche Sammlung von Mikroorganismen andZellkulturen GmbH (DSMZ), Centraalbureau Voor Schimmelcultures (CBS),and Agricultural Research Service Patent Culture Collection, NorthernRegional Research Center (NRRL).

The polypeptide may be identified and obtained from other sourcesincluding microorganisms isolated from nature (e.g., soil, composts,water, etc.) or DNA samples obtained directly from natural materials(e.g., soil, composts, water, etc.) using the above-mentioned probes.Techniques for isolating microorganisms and DNA directly from naturalhabitats are well known in the art. A polynucleotide encoding thepolypeptide may then be obtained by similarly screening a genomic DNA orcDNA library of another microorganism or mixed DNA sample. Once apolynucleotide encoding a polypeptide has been detected with theprobe(s), the polynucleotide can be isolated or cloned by utilizingtechniques that are known to those of ordinary skill in the art (see,e.g., Sambrook et al., 1989, supra).

Catalytic Domains

In one embodiment, the present invention also relates to catalyticdomains having a sequence identity to amino acids 19 to 397 of SEQ IDNO: 2 of at least 75%, at least 80%, at least 85%, at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100%. In one aspect, the catalytic domains comprise amino acid sequencesthat differ by no more than 10 amino acids, e.g., 1, 2, 3, 4, 5, 6, 7,8, or 9, from amino acids 19 to 397 of SEQ ID NO: 2.

The catalytic domain preferably comprises or consists of amino acids 19to 397 of SEQ ID NO: 2 or an allelic variant thereof; or is a fragmentthereof having endoglucanase activity.

In another embodiment, the present invention also relates to catalyticdomains encoded by polynucleotides that hybridize under high stringencyconditions, or very high stringency conditions (as defined above) with(i) the nucleotides 55 to 1191 of SEQ ID NO: 1, or (ii) the full-lengthcomplement of (i) (Sambrook et al., 1989, supra).

In another embodiment, the present invention also relates to catalyticdomains encoded by polynucleotides having a sequence identity tonucleotides 55 to 1191 of SEQ ID NO: 1 at least 75%, at least 80%, atleast 85%, at least 90%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100%.

The polynucleotide encoding the catalytic domain preferably comprises orconsists of nucleotides 55 to 1191 of SEQ ID NO: 1.

In another embodiment, the present invention also relates to catalyticdomain variants of amino acids 19 to 397 of SEQ ID NO: 2 comprising asubstitution, deletion, and/or insertion at one or more (e.g., several)positions. In one aspect, the number of amino acid substitutions,deletions and/or insertions introduced into the sequence of amino acids19 to 397 of SEQ ID NO: 2 is 10, e.g., 1, 2, 3, 4, 5, 6, 8, or 9.

The catalytic domain according to the invention may further comprise orbe fused to a cellulose binding domain.

Binding Domains

In one embodiment, the present invention also relates to cellulosebinding domains having a sequence identity to amino acids 444 to 477 ofSEQ ID NO: 2 of at least 80%, at least 85%, at least 90%, at least 91%,at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100%. In one aspect, thecellulose binding domains comprise amino acid sequences that differ byno more than 10 amino acids, e.g., 1, 2, 3, 4, 5, 6, 7, 8, or 9, fromamino acids 444 to 477 of SEQ ID NO: 2.

The cellulose binding domain preferably comprises or consists of aminoacids 444 to 477 of SEQ ID NO: 2 or an allelic variant thereof; or is afragment thereof having cellulose binding activity.

In another embodiment, the present invention also relates to cellulosebinding domains encoded by polynucleotides that hybridize under highstringency conditions, or very high stringency conditions (as definedabove) with (i) the nucleotides 1333 to 1431 of SEQ ID NO: 1, or (ii)the full-length complement of (i) (Sambrook et al., 1989, supra).

In another embodiment, the present invention also relates to cellulosebinding domains encoded by polynucleotides having a sequence identity tonucleotides 1333 to 1431 of SEQ ID NO: 1 of at least 80%, at least 85%,at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100%.

The polynucleotide encoding the cellulose binding domain preferablycomprises or consists of nucleotides 1333 to 1431 of SEQ ID NO: 1.

In another embodiment, the present invention also relates to cellulosebinding domain variants of amino acids 444 to 477 of SEQ ID NO: 2comprising a substitution, deletion, and/or insertion at one or more(e.g., several) positions. In one aspect, the number of amino acidsubstitutions, deletions and/or insertions introduced into the sequenceof amino acids 444 to 477 of SEQ ID NO: 2 is 10, e.g., 1, 2, 3, 4, 5, 6,8, or 9.

The binding domain according to the invention is in one embodimentoperably linked to a catalytic domain, e.g., via a linker region. In oneembodiment the linker comprises animo acids 398-443 of SEQ ID NO: 2.

A catalytic domain operably linked to the cellulose binding domain maybe from a hydrolase, isomerase, ligase, lyase, oxidoreductase, ortransferase, e.g., an aminopeptidase, amylase, carbohydrase,carboxypeptidase, catalase, cellobiohydrolase, cellulase, chitinase,cutinase, cyclodextrin glycosyltransferase, deoxyribonuclease,endoglucanase, esterase, alpha-galactosidase, beta-galactosidase,glucoamylase, alpha-glucosidase, beta-glucosidase, invertase, laccase,lipase, mannosidase, mutanase, oxidase, pectinolytic enzyme, peroxidase,phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease,transglutaminase, xylanase, or beta-xylosidase. The polynucleotideencoding the catalytic domain may be obtained from any prokaryotic,eukaryotic, or other source.

Polynucleotides

The present invention also relates to isolated polynucleotides encodingan endoglucanase polypeptide, a catalytic domain, or a cellulose bindingdomain of the present invention, as described herein.

The techniques used to isolate or clone a polynucleotide are known inthe art and include isolation from genomic DNA or cDNA, or a combinationthereof. The cloning of the polynucleotides from genomic DNA can beeffected, e.g., by using the well known polymerase chain reaction (PCR)or antibody screening of expression libraries to detect cloned DNAfragments with shared structural features. See, e.g., Innis et al.,1990, PCR: A Guide to Methods and Application, Academic Press, New York.Other nucleic acid amplification procedures such as ligase chainreaction (LCR), ligation activated transcription (LAT) andpolynucleotide-based amplification (NASBA) may be used. Thepolynucleotides may be cloned from a strain of Talaromyces, or a relatedorganism and thus, for example, may be an allelic or species variant ofthe polypeptide encoding region of the polynucleotide.

Modification of a polynucleotide encoding a polypeptide of the presentinvention may be necessary for synthesizing polypeptides substantiallysimilar to the polypeptide. The term “substantially similar” to thepolypeptide refers to non-naturally occurring forms of the polypeptide.These polypeptides may differ in some engineered way from thepolypeptide isolated from its native source, e.g., variants that differin specific activity, thermostability, pH optimum, or the like. Thevariants may be constructed on the basis of the polynucleotide presentedas the mature polypeptide coding sequence of SEQ ID NO: 1, e.g., asubsequence thereof, and/or by introduction of nucleotide substitutionsthat do not result in a change in the amino acid sequence of thepolypeptide, but which correspond to the codon usage of the hostorganism intended for production of the enzyme, or by introduction ofnucleotide substitutions that may give rise to a different amino acidsequence. For a general description of nucleotide substitution, see,e.g., Ford et al., 1991, Protein Expression and Purification 2: 95-107.

Nucleic Acid Constructs

The present invention also relates to nucleic acid constructs comprisinga polynucleotide of the present invention operably linked to one or morecontrol sequences that direct the expression of the coding sequence in asuitable host cell under conditions compatible with the controlsequences.

A polynucleotide may be manipulated in a variety of ways to provide forexpression of the polypeptide. Manipulation of the polynucleotide priorto its insertion into a vector may be desirable or necessary dependingon the expression vector. The techniques for modifying polynucleotidesutilizing recombinant DNA methods are well known in the art.

The control sequence may be a promoter, a polynucleotide that isrecognized by a host cell for expression of a polynucleotide encoding apolypeptide of the present invention. The promoter containstranscriptional control sequences that mediate the expression of thepolypeptide. The promoter may be any polynucleotide that showstranscriptional activity in the host cell including mutant, truncated,and hybrid promoters, and may be obtained from genes encodingextracellular or intracellular polypeptides either homologous orheterologous to the host cell.

Examples of suitable promoters for directing transcription of thenucleic acid constructs of the present invention in a bacterial hostcell are the promoters obtained from the Bacillus amyloliquefaciensalpha-amylase gene (amyQ), Bacillus licheniformis alpha-amylase gene(amyL), Bacillus licheniformis penicillinase gene (penP), Bacillusstearothermophilus maltogenic amylase gene (amyM), Bacillus subtilislevansucrase gene (sacB), Bacillus subtilis xylA and xylB genes,Bacillus thuringiensis ctyIIIA gene (Agaisse and Lereclus, 1994,Molecular Microbiology 13: 97-107), E. coli lac operon, E. coli trcpromoter (Egon et al., 1988, Gene 69: 301-315), Streptomyces coelicoloragarase gene (dagA), and prokaryotic beta-lactamase gene (VIIIa-Kamaroffet al., 1978, Proc. Natl. Acad. Sci. USA 75: 3727-3731), as well as thetac promoter (DeBoer et al., 1983, Proc. Natl. Acad. Sci. USA 80:21-25). Further promoters are described in “Useful proteins fromrecombinant bacteria” in Gilbert et al., 1980, Scientific American 242:74-94; and in Sambrook et al., 1989, supra. Examples of tandem promotersare disclosed in WO 99/43835.

Examples of suitable promoters for directing transcription of thenucleic acid constructs of the present invention in a filamentous fungalhost cell are promoters obtained from the genes for Aspergillus nidulansacetamidase, Aspergillus niger neutral alpha-amylase, Aspergillus nigeracid stable alpha-amylase, Aspergillus niger or Aspergillus awamoriglucoamylase (glaA), Aspergillus oryzae TAKA amylase, Aspergillus oryzaealkaline protease, Aspergillus oryzae triose phosphate isomerase,Fusarium oxysporum trypsin-like protease (WO 96/00787), Fusariumvenenatum amyloglucosidase (WO 00/56900), Fusarium venenatum Dania (WO00/56900), Fusarium venenatum Quinn (WO 00/56900), Rhizomucor mieheilipase, Rhizomucor miehei aspartic proteinase, Trichoderma reeseibeta-glucosidase, Trichoderma reesei cellobiohydrolase I, Trichodermareesei cellobiohydrolase II, Trichoderma reesei endoglucanase I,Trichoderma reesei endoglucanase II, Trichoderma reesei endoglucanaseIII, Trichoderma reesei endoglucanase IV, Trichoderma reeseiendoglucanase V, Trichoderma reesei xylanase I, Trichoderma reeseixylanase II, Trichoderma reesei beta-xylosidase, as well as the NA2-tpipromoter (a modified promoter from an Aspergillus neutral alpha-amylasegene in which the untranslated leader has been replaced by anuntranslated leader from an Aspergillus triose phosphate isomerase gene;non-limiting examples include modified promoters from an Aspergillusniger neutral alpha-amylase gene in which the untranslated leader hasbeen replaced by an untranslated leader from an Aspergillus nidulans orAspergillus oryzae triose phosphate isomerase gene); and mutant,truncated, and hybrid promoters thereof.

In a yeast host, useful promoters are obtained from the genes forSaccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiaegalactokinase (GAL1), Saccharomyces cerevisiae alcoholdehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH1, ADH2/GAP),Saccharomyces cerevisiae triose phosphate isomerase (TPI), Saccharomycescerevisiae metallothionein (CU P1), and Saccharomyces cerevisiae3-phosphoglycerate kinase. Other useful promoters for yeast host cellsare described by Romanos et al., 1992, Yeast 8: 423-488.

The control sequence may also be a transcription terminator, which isrecognized by a host cell to terminate transcription. The terminator isoperably linked to the 3′-terminus of the polynucleotide encoding thepolypeptide. Any terminator that is functional in the host cell may beused in the present invention.

Preferred terminators for bacterial host cells are obtained from thegenes for Bacillus clausii alkaline protease (aprH), Bacilluslicheniformis alpha-amylase (amyL), and Escherichia coli ribosomal RNA(rrnB).

Preferred terminators for filamentous fungal host cells are obtainedfrom the genes for Aspergillus nidulans anthranilate synthase,Aspergillus niger glucoamylase, Aspergillus niger alpha-glucosidase,Aspergillus oryzae TAKA amylase, and Fusarium oxysporum trypsin-likeprotease.

Preferred terminators for yeast host cells are obtained from the genesfor Saccharomyces cerevisiae enolase, Saccharomyces cerevisiaecytochrome C(CYC1), and Saccharomyces cerevisiaeglyceraldehyde-3-phosphate dehydrogenase. Other useful terminators foryeast host cells are described by Romanos et al., 1992, supra.

The control sequence may also be an mRNA stabilizer region downstream ofa promoter and upstream of the coding sequence of a gene which increasesexpression of the gene.

Examples of suitable mRNA stabilizer regions are obtained from aBacillus thuringiensis cryIIIA gene (WO 94/25612) and a Bacillussubtilis SP82 gene (Hue et al., 1995, Journal of Bacteriology 177:3465-3471).

The control sequence may also be a leader, a nontranslated region of anmRNA that is important for translation by the host cell. The leader isoperably linked to the 5′-terminus of the polynucleotide encoding thepolypeptide. Any leader that is functional in the host cell may be used.

Preferred leaders for filamentous fungal host cells are obtained fromthe genes for Aspergillus oryzae TAKA amylase and Aspergillus nidulanstriose phosphate isomerase.

Suitable leaders for yeast host cells are obtained from the genes forSaccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha-factor, andSaccharomyces cerevisiae alcoholdehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).

The control sequence may also be a polyadenylation sequence, a sequenceoperably linked to the 3′-terminus of the polynucleotide and, whentranscribed, is recognized by the host cell as a signal to addpolyadenosine residues to transcribed mRNA. Any polyadenylation sequencethat is functional in the host cell may be used.

Preferred polyadenylation sequences for filamentous fungal host cellsare obtained from the genes for Aspergillus nidulans anthranilatesynthase, Aspergillus niger glucoamylase, Aspergillus nigeralpha-glucosidase Aspergillus oryzae TAKA amylase, and Fusariumoxysporum trypsin-like protease.

Useful polyadenylation sequences for yeast host cells are described byGuo and Sherman, 1995, Mol. Cellular. Biol. 15: 5983-5990.

The control sequence may also be a signal peptide coding region thatencodes a signal peptide linked to the N-terminus of a polypeptide anddirects the polypeptide into the cell's secretory pathway. The 5′-end ofthe coding sequence of the polynucleotide may inherently contain asignal peptide coding sequence naturally linked in translation readingframe with the segment of the coding sequence that encodes thepolypeptide. Alternatively, the 5′-end of the coding sequence maycontain a signal peptide coding sequence that is foreign to the codingsequence. A foreign signal peptide coding sequence may be required wherethe coding sequence does not naturally contain a signal peptide codingsequence. Alternatively, a foreign signal peptide coding sequence maysimply replace the natural signal peptide coding sequence in order toenhance secretion of the polypeptide. However, any signal peptide codingsequence that directs the expressed polypeptide into the secretorypathway of a host cell may be used.

Effective signal peptide coding sequences for bacterial host cells arethe signal peptide coding sequences obtained from the genes for BacillusNCIB 11837 maltogenic amylase, Bacillus licheniformis subtilisin,Bacillus licheniformis beta-lactamase, Bacillus stearothermophilusalpha-amylase, Bacillus stearothermophilus neutral proteases (nprT,nprS, nprM), and Bacillus subtilis prsA. Further signal peptides aredescribed by Simonen and Palva, 1993, Microbiological Reviews 57:109-137.

Effective signal peptide coding sequences for filamentous fungal hostcells are the signal peptide coding sequences obtained from the genesfor Aspergillus niger neutral amylase, Aspergillus niger glucoamylase,Aspergillus oryzae TAKA amylase, Humicola insolens cellulase, Humicolainsolens endoglucanase V, Humicola lanuginosa lipase, and Rhizomucormiehei aspartic proteinase.

Useful signal peptides for yeast host cells are obtained from the genesfor Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiaeinvertase. Other useful signal peptide coding sequences are described byRomanos et al., 1992, supra.

The control sequence may also be a propeptide coding sequence thatencodes a propeptide positioned at the N-terminus of a polypeptide. Theresultant polypeptide is known as a proenzyme or propolypeptide (or azymogen in some cases). A propolypeptide is generally inactive and canbe converted to an active polypeptide by catalytic or autocatalyticcleavage of the propeptide from the propolypeptide. The propeptidecoding sequence may be obtained from the genes for Bacillus subtilisalkaline protease (aprE), Bacillus subtilis neutral protease (nprT),Myceliophthora thermophila laccase (WO 95/33836), Rhizomucor mieheiaspartic proteinase, and Saccharomyces cerevisiae alpha-factor.

Where both signal peptide and propeptide sequences are present, thepropeptide sequence is positioned next to the N-terminus of apolypeptide and the signal peptide sequence is positioned next to theN-terminus of the propeptide sequence.

It may also be desirable to add regulatory sequences that regulateexpression of the polypeptide relative to the growth of the host cell.Examples of regulatory systems are those that cause expression of thegene to be turned on or off in response to a chemical or physicalstimulus, including the presence of a regulatory compound. Regulatorysystems in prokaryotic systems include the lac, tac, and trp operatorsystems. In yeast, the ADH2 system or GAL1 system may be used. Infilamentous fungi, the Aspergillus niger glucoamylase promoter,Aspergillus oryzae TAKA alpha-amylase promoter, and Aspergillus oryzaeglucoamylase promoter may be used. Other examples of regulatorysequences are those that allow for gene amplification. In eukaryoticsystems, these regulatory sequences include the dihydrofolate reductasegene that is amplified in the presence of methotrexate, and themetallothionein genes that are amplified with heavy metals.

In these cases, the polynucleotide encoding the polypeptide would beoperably linked with the regulatory sequence.

Expression Vectors

The present invention also relates to recombinant expression vectorscomprising a polynucleotide of the present invention operably linked toone or more control sequences, e.g., a promoter, and transcriptional andtranslational stop signals. The various nucleotide and control sequencesmay be joined together to produce a recombinant expression vector thatmay include one or more convenient restriction sites to allow forinsertion or substitution of the polynucleotide encoding the polypeptideat such sites. Alternatively, the polynucleotide may be expressed byinserting the polynucleotide or a nucleic acid construct comprising thepolynucleotide into an appropriate vector for expression. In creatingthe expression vector, the coding sequence is located in the vector sothat the coding sequence is operably linked with the appropriate controlsequences for expression.

The recombinant expression vector may be any vector (e.g., a plasmid orvirus) that can be conveniently subjected to recombinant DNA proceduresand can bring about expression of the polynucleotide. The choice of thevector will typically depend on the compatibility of the vector with thehost cell into which the vector is to be introduced. The vector may be alinear or closed circular plasmid.

The vector may be an autonomously replicating vector, i.e., a vectorthat exists as an extrachromosomal entity, the replication of which isindependent of chromosomal replication, e.g., a plasmid, anextrachromosomal element, a minichromosome, or an artificial chromosome.The vector may contain any means for assuring self-replication.Alternatively, the vector may be one that, when introduced into the hostcell, is integrated into the genome and replicated together with thechromosome(s) into which it has been integrated. Furthermore, a singlevector or plasmid or two or more vectors or plasmids that togethercontain the total DNA to be introduced into the genome of the host cell,or a transposon, may be used.

The vector preferably contains one or more selectable markers thatpermit easy selection of transformed, transfected, transduced, or thelike cells. A selectable marker is a gene the product of which providesfor biocide or viral resistance, resistance to heavy metals, prototrophyto auxotrophs, and the like.

Examples of bacterial selectable markers are Bacillus licheniformis orBacillus subtilis dal genes, or markers that confer antibioticresistance such as ampicillin, chloramphenicol, kanamycin, neomycin,spectinomycin, or tetracycline resistance. Suitable markers for yeasthost cells include, but are not limited to, ADE2, HIS3, LEU2, LYS2,MET3, TRP1, and URA3. Selectable markers for use in a filamentous fungalhost cell include, but are not limited to, amdS (acetamidase), argB(ornithine carbamoyltransferase), bar (phosphinothricinacetyltransferase), hph (hygromycin phosphotransferase), niaD (nitratereductase), pyrG (orotidine-5′-phosphate decarboxylase), sC (sulfateadenyltransferase), and trpC (anthranilate synthase), as well asequivalents thereof. Preferred for use in an Aspergillus cell areAspergillus nidulans or Aspergillus oryzae amdS and pyrG genes and aStreptomyces hygroscopicus bar gene.

The vector preferably contains an element(s) that permits integration ofthe vector into the host cell's genome or autonomous replication of thevector in the cell independent of the genome.

For integration into the host cell genome, the vector may rely on thepolynucleotide's sequence encoding the polypeptide or any other elementof the vector for integration into the genome by homologous ornon-homologous recombination. Alternatively, the vector may containadditional polynucleotides for directing integration by homologousrecombination into the genome of the host cell at a precise location(s)in the chromosome(s). To increase the likelihood of integration at aprecise location, the integrational elements should contain a sufficientnumber of nucleic acids, such as 100 to 10,000 base pairs, 400 to 10,000base pairs, and 800 to 10,000 base pairs, which have a high degree ofsequence identity to the corresponding target sequence to enhance theprobability of homologous recombination. The integrational elements maybe any sequence that is homologous with the target sequence in thegenome of the host cell. Furthermore, the integrational elements may benon-encoding or encoding polynucleotides. On the other hand, the vectormay be integrated into the genome of the host cell by non-homologousrecombination.

For autonomous replication, the vector may further comprise an origin ofreplication enabling the vector to replicate autonomously in the hostcell in question. The origin of replication may be any plasmidreplicator mediating autonomous replication that functions in a cell.The term “origin of replication” or “plasmid replicator” means apolynucleotide that enables a plasmid or vector to replicate in vivo.

Examples of bacterial origins of replication are the origins ofreplication of plasmids pBR322, pUC19, pACYC177, and pACYC184 permittingreplication in E. coli, and pUB110, pE194, pTA1060, and pAMR1 permittingreplication in Bacillus.

Examples of origins of replication for use in a yeast host cell are the2 micron origin of replication, ARS1, ARS4, the combination of ARS1 andCEN3, and the combination of ARS4 and CEN6.

Examples of origins of replication useful in a filamentous fungal cellare AMA1 and ANSI (Gems et al., 1991, Gene 98: 61-67; Cullen et al.,1987, Nucleic Acids Res. 15: 9163-9175; WO 00/24883). Isolation of theAMA1 gene and construction of plasmids or vectors comprising the genecan be accomplished according to the methods disclosed in WO 00/24883.

More than one copy of a polynucleotide of the present invention may beinserted into a host cell to increase production of a polypeptide. Anincrease in the copy number of the polynucleotide can be obtained byintegrating at least one additional copy of the sequence into the hostcell genome or by including an amplifiable selectable marker gene withthe polynucleotide where cells containing amplified copies of theselectable marker gene, and thereby additional copies of thepolynucleotide, can be selected for by cultivating the cells in thepresence of the appropriate selectable agent.

The procedures used to ligate the elements described above to constructthe recombinant expression vectors of the present invention are wellknown to one skilled in the art (see, e.g., Sambrook et al., 1989,supra).

Host Cells

The present invention also relates to recombinant host cells, comprisinga polynucleotide of the present invention operably linked to one or morecontrol sequences that direct the production of a polypeptide of thepresent invention. A construct or vector comprising a polynucleotide isintroduced into a host cell so that the construct or vector ismaintained as a chromosomal integrant or as a self-replicatingextra-chromosomal vector as described earlier. The term “host cell”encompasses any progeny of a parent cell that is not identical to theparent cell due to mutations that occur during replication. The choiceof a host cell will to a large extent depend upon the gene encoding thepolypeptide and its source.

The host cell may be any cell useful in the recombinant production of apolypeptide of the present invention, e.g., a prokaryote or a eukaryote.

The prokaryotic host cell may be any Gram-positive or Gram-negativebacterium. Gram-positive bacteria include, but are not limited to,Bacillus, Clostridium, Enterococcus, Geobacillus, Lactobacillus,Lactococcus, Oceanobacillus, Staphylococcus, Streptococcus, andStreptomyces. Gram-negative bacteria include, but are not limited to,Campylobacter, E. coli, Flavobacterium, Fusobacterium, Helicobacter,Ilyobacter, Neisseria, Pseudomonas, Salmonella, and Ureaplasma.

The bacterial host cell may be any Bacillus cell including, but notlimited to, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillusbrevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans,Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacilluslicheniformis, Bacillus megaterium, Bacillus pumilus, Bacillusstearothermophilus, Bacillus subtilis, and Bacillus thuringiensis cells.

The bacterial host cell may also be any Streptococcus cell including,but not limited to, Streptococcus equisimilis, Streptococcus pyogenes,Streptococcus uberis, and Streptococcus equi subsp. Zooepidemicus cells.

The bacterial host cell may also be any Streptomyces cell including, butnot limited to, Streptomyces achromogenes, Streptomyces avermitilis,Streptomyces coelicolor, Streptomyces griseus, and Streptomyces lividanscells.

The introduction of DNA into a Bacillus cell may be effected byprotoplast transformation (see, e.g., Chang and Cohen, 1979, Mol. Gen.Genet. 168: 111-115), competent cell transformation (see, e.g., Youngand Spizizen, 1961, J. Bacteriol. 81: 823-829, or Dubnau andDavidoff-Abelson, 1971, J. Mol. Biol. 56: 209-221), electroporation(see, e.g., Shigekawa and Dower, 1988, Biotechniques 6: 742-751), orconjugation (see, e.g., Koehler and Thorne, 1987, J. Bacteriol. 169:5271-5278). The introduction of DNA into an E. coli cell may be effectedby protoplast transformation (see, e.g., Hanahan, 1983, J. Mol. Biol.166: 557-580) or electroporation (see, e.g., Dower et al., 1988, NucleicAcids Res. 16: 6127-6145). The introduction of DNA into a Streptomycescell may be effected by protoplast transformation, electroporation (see,e.g., Gong et al., 2004, Folia Microbiol. (Praha) 49: 399-405),conjugation (see, e.g., Mazodier et al., 1989, J. Bacteriol. 171:3583-3585), or transduction (see, e.g., Burke et al., 2001, Proc. Natl.Acad. Sci. USA 98: 6289-6294). The introduction of DNA into aPseudomonas cell may be effected by electroporation (see, e.g., Choi etal., 2006, J. Microbiol. Methods 64: 391-397) or conjugation (see, e.g.,Pinedo and Smets, 2005, Appl. Environ. Microbiol. 71: 51-57). Theintroduction of DNA into a Streptococcus cell may be effected by naturalcompetence (see, e.g., Perry and Kuramitsu, 1981, Infect. Immun. 32:1295-1297), protoplast transformation (see, e.g., Catt and Jollick,1991, Microbios 68: 189-207), electroporation (see, e.g., Buckley etal., 1999, Appl. Environ. Microbiol. 65: 3800-3804), or conjugation(see, e.g., Clewell, 1981, Microbiol. Rev. 45: 409-436). However, anymethod known in the art for introducing DNA into a host cell can beused.

The host cell may also be a eukaryote, such as a mammalian, insect,plant, or fungal cell.

The host cell may be a fungal cell. “Fungi” as used herein includes thephyla Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota as wellas the Oomycota and all mitosporic fungi (as defined by Hawksworth etal., In, Ainsworth and Bisby's Dictionary of The Fungi, 8th edition,1995, CAB International, University Press, Cambridge, UK).

The fungal host cell may be a yeast cell. “Yeast” as used hereinincludes ascosporogenous yeast (Endomycetales), basidiosporogenousyeast, and yeast belonging to the Fungi Imperfecti (Blastomycetes).Since the classification of yeast may change in the future, for thepurposes of this invention, yeast shall be defined as described inBiology and Activities of Yeast (Skinner, Passmore, and Davenport,editors, Soc. App. Bacteriol. Symposium Series No. 9, 1980).

The yeast host cell may be a Candida, Hansenula, Kluyveromyces, Pichia,Saccharomyces, Schizosaccharomyces, or Yarrowia cell, such as aKluyveromyces lactis, Saccharomyces carlsbergensis, Saccharomycescerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii,Saccharomyces kluyveri, Saccharomyces norbensis, Saccharomycesoviformis, or Yarrowia lipolytica cell.

The fungal host cell may be a filamentous fungal cell. “Filamentousfungi” include all filamentous forms of the subdivision Eumycota andOomycota (as defined by Hawksworth et al., 1995, supra). The filamentousfungi are generally characterized by a mycelial wall composed of chitin,cellulose, glucan, chitosan, mannan, and other complex polysaccharides.Vegetative growth is by hyphal elongation and carbon catabolism isobligately aerobic. In contrast, vegetative growth by yeasts such asSaccharomyces cerevisiae is by budding of a unicellular thallus andcarbon catabolism may be fermentative.

The filamentous fungal host cell may be an Acremonium, Aspergillus,Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysosporium, Coprinus,Coriolus, Cryptococcus, Filibasidium, Fusarium, Humicola, Magnaporthe,Mucor, Myceliophthora, Neocallimastix, Neurospora, Paecilomyces,Penicillium, Phanerochaete, Phlebia, Piromyces, Pleurotus,Schizophyllum, Talaromyces, Thermoascus, Thielavia, Tolypocladium,Trametes, or Trichoderma cell.

For example, the filamentous fungal host cell may be an Aspergillusawamori, Aspergillus foetidus, Aspergillus fumigatus, Aspergillusjaponicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae,Bjerkandera adusta, Ceriporiopsis aneirina, Ceriporiopsis caregiea,Ceriporiopsis gilvescens, Ceriporiopsis pannocinta, Ceriporiopsisrivulosa, Ceriporiopsis subrufa, Ceriporiopsis subvermispora,Chrysosporium inops, Chrysosporium keratinophilum, Chrysosporiumlucknowense, Chrysosporium merdarium, Chrysosporium pannicola,Chrysosporium queenslandicum, Chrysosporium tropicum, Chrysosporiumzonatum, Coprinus cinereus, Coriolus hirsutus, Fusarium bactridioides,Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusariumgraminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi,Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusariumsambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusariumsulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusariumvenenatum, Humicola insolens, Humicola lanuginosa, Mucor miehei,Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum,Phanerochaete chrysosporium, Phlebia radiata, Pleurotus eryngii,Thielavia terrestris, Trametes villosa, Trametes versicolor, Trichodermaharzianum, Trichoderma koningii, Trichoderma longibrachiatum,Trichoderma reesei, or Trichoderma viride cell.

Fungal cells may be transformed by a process involving protoplastformation, transformation of the protoplasts, and regeneration of thecell wall in a manner known per se. Suitable procedures fortransformation of Aspergillus and Trichoderma host cells are describedin EP 238023, Yelton et al., 1984, Proc. Natl. Acad. Sci. USA 81:1470-1474, and Christensen et al., 1988, Bio/Technology 6: 1419-1422.Suitable methods for transforming Fusarium species are described byMalardier et al., 1989, Gene 78: 147-156, and WO 96/00787. Yeast may betransformed using the procedures described by Becker and Guarente, InAbelson, J. N. and Simon, M. I., editors, Guide to Yeast Genetics andMolecular Biology, Methods in Enzymology, Volume 194, pp 182-187,Academic Press, Inc., New York; Ito et al., 1983, J. Bacteriol. 153:163; and Hinnen et al., 1978, Proc. Natl. Acad. Sci. USA 75: 1920.

Methods of Production

The present invention also relates to methods of producing a polypeptideof the present invention, comprising (a) cultivating a cell, which inits wild-type form produces the polypeptide, under conditions conducivefor production of the polypeptide; and (b) recovering the polypeptide.In a preferred aspect, the cell is a Talaromyces cell. In a morepreferred aspect, the cell is a Talaromyces leycettanus cell. In a mostpreferred aspect, the cell is Talaromyces leycettanus CBS398.68.

The present invention also relates to methods of producing a polypeptideof the present invention, comprising (a) cultivating a recombinant hostcell of the present invention under conditions conducive for productionof the polypeptide; and (b) recovering the polypeptide.

The host cells are cultivated in a nutrient medium suitable forproduction of the polypeptide using methods known in the art. Forexample, the cell may be cultivated by shake flask cultivation, orsmall-scale or large-scale fermentation (including continuous, batch,fed-batch, or solid state fermentations) in laboratory or industrialfermentors performed in a suitable medium and under conditions allowingthe polypeptide to be expressed and/or isolated. The cultivation takesplace in a suitable nutrient medium comprising carbon and nitrogensources and inorganic salts, using procedures known in the art. Suitablemedia are available from commercial suppliers or may be preparedaccording to published compositions (e.g., in catalogues of the AmericanType Culture Collection). If the polypeptide is secreted into thenutrient medium, the polypeptide can be recovered directly from themedium. If the polypeptide is not secreted, it can be recovered fromcell lysates.

The polypeptide may be detected using methods known in the art that arespecific for the polypeptides having endoglucanase activity. Thesedetection methods include, but are not limited to, use of specificantibodies, formation of an enzyme product, or disappearance of anenzyme substrate. For example, an enzyme assay may be used to determinethe activity of the polypeptide.

The polypeptide may be recovered using methods known in the art. Forexample, the polypeptide may be recovered from the nutrient medium byconventional procedures including, but not limited to, collection,centrifugation, filtration, extraction, spray-drying, evaporation, orprecipitation.

The polypeptide may be purified by a variety of procedures known in theart including, but not limited to, chromatography (e.g., ion exchange,affinity, hydrophobic, chromatofocusing, and size exclusion),electrophoretic procedures (e.g., preparative isoelectric focusing),differential solubility (e.g., ammonium sulfate precipitation),SDS-PAGE, or extraction (see, e.g., Protein Purification, Janson andRyden, editors, VCH Publishers, New York, 1989) to obtain substantiallypure polypeptides.

In an alternative aspect, the polypeptide is not recovered, but rather ahost cell of the present invention expressing the polypeptide is used asa source of the polypeptide.

Plants

The present invention also relates to isolated plants, e.g., atransgenic plant, plant part, or plant cell, comprising a polynucleotideof the present invention so as to express and produce a polypeptide ordomain in recoverable quantities. The polypeptide or domain may berecovered from the plant or plant part. Alternatively, the plant orplant part containing the polypeptide or domain may be used as such forimproving the quality of a food or feed, e.g., improving nutritionalvalue, palatability, and rheological properties, or to destroy anantinutritive factor.

The transgenic plant can be dicotyledonous (a dicot) or monocotyledonous(a monocot). Examples of monocot plants are grasses, such as meadowgrass (blue grass, Poa), forage grass such as Festuca, Lolium, temperategrass, such as Agrostis, and cereals, e.g., wheat, oats, rye, barley,rice, sorghum, and maize (corn).

Examples of dicot plants are tobacco, legumes, such as lupins, potato,sugar beet, pea, bean and soybean, and cruciferous plants (familyBrassicaceae), such as cauliflower, rape seed, and the closely relatedmodel organism Arabidopsis thaliana.

Examples of plant parts are stem, callus, leaves, root, fruits, seeds,and tubers as well as the individual tissues comprising these parts,e.g., epidermis, mesophyll, parenchyme, vascular tissues, meristems.Specific plant cell compartments, such as chloroplasts, apoplasts,mitochondria, vacuoles, peroxisomes and cytoplasm are also considered tobe a plant part. Furthermore, any plant cell, whatever the tissueorigin, is considered to be a plant part. Likewise, plant parts such asspecific tissues and cells isolated to facilitate the utilization of theinvention are also considered plant parts, e.g., embryos, endosperms,aleurone and seed coats.

Also included within the scope of the present invention are the progenyof such plants, plant parts, and plant cells.

The transgenic plant or plant cell expressing the polypeptide or domainmay be constructed in accordance with methods known in the art. Inshort, the plant or plant cell is constructed by incorporating one ormore expression constructs encoding the polypeptide or domain into theplant host genome or chloroplast genome and propagating the resultingmodified plant or plant cell into a transgenic plant or plant cell.

The expression construct is conveniently a nucleic acid construct thatcomprises a polynucleotide encoding a polypeptide or domain operablylinked with appropriate regulatory sequences required for expression ofthe polynucleotide in the plant or plant part of choice. Furthermore,the expression construct may comprise a selectable marker useful foridentifying plant cells into which the expression construct has beenintegrated and DNA sequences necessary for introduction of the constructinto the plant in question (the latter depends on the DNA introductionmethod to be used).

The choice of regulatory sequences, such as promoter and terminatorsequences and optionally signal or transit sequences, is determined, forexample, on the basis of when, where, and how the polypeptide or domainis desired to be expressed. For instance, the expression of the geneencoding a polypeptide or domain may be constitutive or inducible, ormay be developmental, stage or tissue specific, and the gene product maybe targeted to a specific tissue or plant part such as seeds or leaves.Regulatory sequences are, for example, described by Tague et al., 1988,Plant Physiology 86: 506.

For constitutive expression, the ³⁵S-CaMV, the maize ubiquitin 1, or therice actin 1 promoter may be used (Franck et al., 1980, Cell 21:285-294; Christensen et al., 1992, Plant Mol. Biol. 18: 675-689; Zhanget al., 1991, Plant Cell 3: 1155-1165). Organ-specific promoters may be,for example, a promoter from storage sink tissues such as seeds, potatotubers, and fruits (Edwards and Coruzzi, 1990, Ann. Rev. Genet. 24:275-303), or from metabolic sink tissues such as meristems (Ito et al.,1994, Plant Mol. Biol. 24: 863-878), a seed specific promoter such asthe glutelin, prolamin, globulin, or albumin promoter from rice (Wu etal., 1998, Plant Cell Physiol. 39: 885-889), a Vicia faba promoter fromthe legumin B4 and the unknown seed protein gene from Vicia faba (Conradet al., 1998, J. Plant Physiol. 152: 708-711), a promoter from a seedoil body protein (Chen et al., 1998, Plant Cell Physiol. 39: 935-941),the storage protein napA promoter from Brassica napus, or any other seedspecific promoter known in the art, e.g., as described in WO 91/14772.Furthermore, the promoter may be a leaf specific promoter such as therbcs promoter from rice or tomato (Kyozuka et al., 1993, Plant Physiol.102: 991-1000), the chlorella virus adenine methyltransferase genepromoter (Mitra and Higgins, 1994, Plant Mol. Biol. 26: 85-93), the aldPgene promoter from rice (Kagaya et al., 1995, Mol. Gen. Genet. 248:668-674), or a wound inducible promoter such as the potato pin2 promoter(Xu et al., 1993, Plant Mol. Biol. 22: 573-588). Likewise, the promotermay be induced by abiotic treatments such as temperature, drought, oralterations in salinity or induced by exogenously applied substancesthat activate the promoter, e.g., ethanol, oestrogens, plant hormonessuch as ethylene, abscisic acid, and gibberellic acid, and heavy metals.

A promoter enhancer element may also be used to achieve higherexpression of a polypeptide or domain in the plant. For instance, thepromoter enhancer element may be an intron that is placed between thepromoter and the polynucleotide encoding a polypeptide or domain. Forinstance, Xu et al., 1993, supra, disclose the use of the first intronof the rice actin 1 gene to enhance expression.

The selectable marker gene and any other parts of the expressionconstruct may be chosen from those available in the art.

The nucleic acid construct is incorporated into the plant genomeaccording to conventional techniques known in the art, includingAgrobacterium-mediated transformation, virus-mediated transformation,microinjection, particle bombardment, biolistic transformation, andelectroporation (Gasser et al., 1990, Science 244: 1293; Potrykus, 1990,Bio/Technology 8: 535; Shimamoto et al., 1989, Nature 338: 274).

Agrobacterium tumefaciens-mediated gene transfer is a method forgenerating transgenic dicots (for a review, see Hooykas andSchilperoort, 1992, Plant Mol. Biol. 19: 15-38) and for transformingmonocots, although other transformation methods may be used for theseplants. A method for generating transgenic monocots is particlebombardment (microscopic gold or tungsten particles coated with thetransforming DNA) of embryonic calli or developing embryos (Christou,1992, Plant J. 2: 275-281; Shimamoto, 1994, Curr. Opin. Biotechnol. 5:158-162; Vasil et al., 1992, Bio/Technology 10: 667-674). An alternativemethod for transformation of monocots is based on protoplasttransformation as described by Omirulleh et al., 1993, Plant Mol. Biol.21: 415-428. Additional transformation methods include those describedin U.S. Pat. Nos. 6,395,966 and 7,151,204 (both of which are hereinincorporated by reference in their entirety).

Following transformation, the transformants having incorporated theexpression construct are selected and regenerated into whole plantsaccording to methods well known in the art. Often the transformationprocedure is designed for the selective elimination of selection geneseither during regeneration or in the following generations by using, forexample, co-transformation with two separate T-DNA constructs or sitespecific excision of the selection gene by a specific recombinase.

In addition to direct transformation of a particular plant genotype witha construct of the present invention, transgenic plants may be made bycrossing a plant having the construct to a second plant lacking theconstruct. For example, a construct encoding a polypeptide or domain canbe introduced into a particular plant variety by crossing, without theneed for ever directly transforming a plant of that given variety.Therefore, the present invention encompasses not only a plant directlyregenerated from cells which have been transformed in accordance withthe present invention, but also the progeny of such plants. As usedherein, progeny may refer to the offspring of any generation of a parentplant prepared in accordance with the present invention. Such progenymay include a DNA construct prepared in accordance with the presentinvention. Crossing results in the introduction of a transgene into aplant line by cross pollinating a starting line with a donor plant line.Non-limiting examples of such steps are described in U.S. Pat. No.7,151,204.

Plants may be generated through a process of backcross conversion. Forexample, plants include plants referred to as a backcross convertedgenotype, line, inbred, or hybrid.

Genetic markers may be used to assist in the introgression of one ormore transgenes of the invention from one genetic background intoanother. Marker assisted selection offers advantages relative toconventional breeding in that it can be used to avoid errors caused byphenotypic variations. Further, genetic markers may provide dataregarding the relative degree of elite germplasm in the individualprogeny of a particular cross. For example, when a plant with a desiredtrait which otherwise has a non-agronomically desirable geneticbackground is crossed to an elite parent, genetic markers may be used toselect progeny which not only possess the trait of interest, but alsohave a relatively large proportion of the desired germplasm. In thisway, the number of generations required to introgress one or more traitsinto a particular genetic background is minimized.

The present invention also relates to methods of producing a polypeptideor domain of the present invention comprising (a) cultivating atransgenic plant or a plant cell comprising a polynucleotide encodingthe polypeptide or domain under conditions conducive for production ofthe polypeptide or domain; and (b) recovering the polypeptide or domain.

Compositions

The present invention also relates to compositions comprising apolypeptide of the present invention. Preferably, the compositions areenriched in such a polypeptide. The term “enriched” indicates that theendoglucanase activity of the composition has been increased, e.g., withan enrichment factor of at least 1.1.

The composition may comprise a polypeptide of the present invention asthe major enzymatic component, e.g., a mono-component composition.Alternatively, the composition may comprise multiple enzymaticactivities, such as one or more (e.g., several) enzymes selected fromthe group consisting of a cellulase, a hemicellulase, GH61 polypeptide,an expansin, an esterase, a laccase, a ligninolytic enzyme, a pectinase,a peroxidase, a protease, and a swollenin. Preferably, the compositioncomprises the endoglucanase according to the invention and at least acellobiohydrolase and a beta-glucosidase. In a most preferred embodimentthe composition comprises the endoglucanase according to the inventionand at least a cellobiohydrolase and a beta-glucosidase and a GH61family polypeptide having cellulolytic enhancing activity.

The polypeptide compositions may be prepared in accordance with methodsknown in the art and may be in the form of a liquid or a drycomposition. For instance, the polypeptide composition may be in theform of a granulate or a microgranulate. The polypeptide to be includedin the composition may be stabilized in accordance with methods known inthe art.

Examples are given below of preferred uses of the polypeptidecompositions of the invention. The dosage of the polypeptide compositionof the invention and other conditions under which the composition isused may be determined on the basis of methods known in the art.

Methods of Processing Cellulosic Material

The present invention also relates to methods for degrading orconverting a cellulosic material, comprising: treating the cellulosicmaterial with an enzyme composition in the presence of a polypeptidehaving endoglucanase activity of the present invention. In a preferredaspect, the method further comprises recovering the degraded orconverted cellulosic material.

The present invention also relates to methods of producing afermentation product, comprising: (a) saccharifying a cellulosicmaterial with an enzyme composition in the presence of a polypeptidehaving endoglucanase activity of the present invention; (b) fermentingthe saccharified cellulosic material with one or more (several)fermenting microorganisms to produce the fermentation product; and (c)recovering the fermentation product from the fermentation.

The present invention also relates to methods of fermenting a cellulosicmaterial, comprising: fermenting the cellulosic material with one ormore (several) fermenting microorganisms, wherein the cellulosicmaterial is saccharified with an enzyme composition in the presence of apolypeptide having endoglucanase activity of the present invention. In apreferred aspect, the fermenting of the cellulosic material produces afermentation product. In another preferred aspect, the method furthercomprises recovering the fermentation product from the fermentation.

The methods of the present invention can be used to saccharify acellulosic material to fermentable sugars and convert the fermentablesugars to many useful substances, e.g., fuel, potable ethanol, and/orfermentation products (e.g., acids, alcohols, ketones, gases, and thelike). The production of a desired fermentation product from cellulosicmaterial typically involves pretreatment, enzymatic hydrolysis(saccharification), and fermentation.

The processing of cellulosic material according to the present inventioncan be accomplished using processes conventional in the art. Moreover,the methods of the present invention can be implemented using anyconventional biomass processing apparatus configured to operate inaccordance with the invention.

Hydrolysis (saccharification) and fermentation, separate orsimultaneous, include, but are not limited to, separate hydrolysis andfermentation (SHF); simultaneous saccharification and fermentation(SSF); simultaneous saccharification and cofermentation (SSCF); hybridhydrolysis and fermentation (HHF); separate hydrolysis andco-fermentation (SHCF); hybrid hydrolysis and co-fermentation (HHCF);and direct microbial conversion (DMC). SHF uses separate process stepsto first enzymatically hydrolyze cellulosic material to fermentablesugars, e.g., glucose, cellobiose, cellotriose, and pentose sugars, andthen ferment the fermentable sugars to ethanol. In SSF, the enzymatichydrolysis of cellulosic material and the fermentation of sugars toethanol are combined in one step (Philippidis, G. P., 1996, Cellulosebioconversion technology, in Handbook on Bioethanol: Production andUtilization, Wyman, C. E., ed., Taylor & Francis, Washington, D.C.,179-212). SSCF involves the cofermentation of multiple sugars (Sheehanand Himmel, 1999, Enzymes, energy and the environment: A strategicperspective on the U.S. Department of Energy's research and developmentactivities for bioethanol, Biotechnol. Prog. 15: 817-827). HHF involvesa separate hydrolysis step, and in addition a simultaneoussaccharification and hydrolysis step, which can be carried out in thesame reactor. The steps in an HHF process can be carried out atdifferent temperatures, i.e., high temperature enzymaticsaccharification followed by SSF at a lower temperature that thefermentation strain can tolerate. DMC combines all three processes(enzyme production, hydrolysis, and fermentation) in one or more(several) steps where the same organism is used to produce the enzymesfor conversion of the cellulosic material to fermentable sugars and toconvert the fermentable sugars into a final product (Lynd et al., 2002,Microbial cellulose utilization: Fundamentals and biotechnology,Microbiol. Mol. Biol. Reviews 66: 506-577). It is understood herein thatany method known in the art comprising pretreatment, enzymatichydrolysis (saccharification), fermentation, or a combination thereof,can be used in the practicing the methods of the present invention.

A conventional apparatus can include a fed-batch stirred reactor, abatch stirred reactor, a continuous flow stirred reactor withultrafiltration, and/or a continuous plug-flow column reactor (Corazzaet al., 2003, Optimal control in fed-batch reactor for the cellobiosehydrolysis, Acta Scientiarum. Technology 25: 33-38; Gusakov andSinitsyn, 1985, Kinetics of the enzymatic hydrolysis of cellulose: 1. Amathematical model for a batch reactor process, Enz. Microb. Technol. 7:346-352), an attrition reactor (Ryu and Lee, 1983, Bioconversion ofwaste cellulose by using an attrition bioreactor, Biotechnol. Bioeng.25: 53-65), or a reactor with intensive stirring induced by anelectromagnetic field (Gusakov et al., 1996, Enhancement of enzymaticcellulose hydrolysis using a novel type of bioreactor with intensivestirring induced by electromagnetic field, Appl. Biochem. Biotechnol.56: 141-153). Additional reactor types include: fluidized bed, upflowblanket, immobilized, and extruder type reactors for hydrolysis and/orfermentation.

Pretreatment.

In practicing the methods of the present invention, any pretreatmentprocess known in the art can be used to disrupt plant cell wallcomponents of cellulosic material (Chandra et al., 2007, Substratepretreatment: The key to effective enzymatic hydrolysis oflignocellulosics? Adv. Biochem. Engin./Biotechnol. 108: 67-93; Galbe andZacchi, 2007, Pretreatment of lignocellulosic materials for efficientbioethanol production, Adv. Biochem. Engin./Biotechnol. 108: 41-65;Hendriks and Zeeman, 2009, Pretreatments to enhance the digestibility oflignocellulosic biomass, Bioresource Technol. 100: 10-18; Mosier et al.,2005, Features of promising technologies for pretreatment oflignocellulosic biomass, Bioresource Technol. 96: 673-686; Taherzadehand Karimi, 2008, Pretreatment of lignocellulosic wastes to improveethanol and biogas production: A review, Int. J. of Mol. Sci. 9:1621-1651; Yang and Wyman, 2008, Pretreatment: the key to unlockinglow-cost cellulosic ethanol, Biofuels Bioproducts andBiorefining-Biofpr. 2: 26-40).

The cellulosic material can also be subjected to particle sizereduction, pre-soaking, wetting, washing, or conditioning prior topretreatment using methods known in the art.

Conventional pretreatments include, but are not limited to, steampretreatment (with or without explosion), dilute acid pretreatment, hotwater pretreatment, alkaline pretreatment, lime pretreatment, wetoxidation, wet explosion, ammonia fiber explosion, organosolvpretreatment, and biological pretreatment. Additional pretreatmentsinclude ammonia percolation, ultrasound, electroporation, microwave,supercritical CO₂, supercritical H₂O, ozone, and gamma irradiationpretreatments.

The cellulosic material can be pretreated before hydrolysis and/orfermentation. Pretreatment is preferably performed prior to thehydrolysis. Alternatively, the pretreatment can be carried outsimultaneously with enzyme hydrolysis to release fermentable sugars,such as glucose, xylose, and/or cellobiose. In most cases thepretreatment step itself results in some conversion of biomass tofermentable sugars (even in absence of enzymes).

Steam Pretreatment. In steam pretreatment, cellulosic material is heatedto disrupt the plant cell wall components, including lignin,hemicellulose, and cellulose to make the cellulose and other fractions,e.g., hemicellulose, accessible to enzymes. Cellulosic material ispassed to or through a reaction vessel where steam is injected toincrease the temperature to the required temperature and pressure and isretained therein for the desired reaction time. Steam pretreatment ispreferably done at 140-230° C., more preferably 160-200° C., and mostpreferably 170-190° C., where the optimal temperature range depends onany addition of a chemical catalyst. Residence time for the steampretreatment is preferably 1-15 minutes, more preferably 3-12 minutes,and most preferably 4-10 minutes, where the optimal residence timedepends on temperature range and any addition of a chemical catalyst.Steam pretreatment allows for relatively high solids loadings, so thatcellulosic material is generally only moist during the pretreatment. Thesteam pretreatment is often combined with an explosive discharge of thematerial after the pretreatment, which is known as steam explosion, thatis, rapid flashing to atmospheric pressure and turbulent flow of thematerial to increase the accessible surface area by fragmentation (Duffand Murray, 1996, Bioresource Technology 855: 1-33; Galbe and Zacchi,2002, Appl. Microbiol. Biotechnol. 59: 618-628; U.S. Patent ApplicationNo. 20020164730). During steam pretreatment, hemicellulose acetyl groupsare cleaved and the resulting acid autocatalyzes partial hydrolysis ofthe hemicellulose to monosaccharides and oligosaccharides. Lignin isremoved to only a limited extent.

A catalyst such as H₂SO₄ or SO₂ (typically 0.3 to 3% w/w) is often addedprior to steam pretreatment, which decreases the time and temperature,increases the recovery, and improves enzymatic hydrolysis (Ballesteroset al., 2006, Appl. Biochem. Biotechnol. 129-132: 496-508; Varga et al.,2004, Appl. Biochem. Biotechnol. 113-116: 509-523; Sassner et al., 2006,Enzyme Microb. Technol. 39: 756-762).

Chemical Pretreatment:

The term “chemical treatment” refers to any chemical pretreatment thatpromotes the separation and/or release of cellulose, hemicellulose,and/or lignin. Examples of suitable chemical pretreatment processesinclude, for example, dilute acid pretreatment, lime pretreatment, wetoxidation, ammonia fiber/freeze explosion (AFEX), ammonia percolation(APR), and organosolv pretreatments.

In dilute acid pretreatment, cellulosic material is mixed with diluteacid, typically H₂SO₄, and water to form a slurry, heated by steam tothe desired temperature, and after a residence time flashed toatmospheric pressure. The dilute acid pretreatment can be performed witha number of reactor designs, e.g., plug-flow reactors, counter-currentreactors, or continuous counter-current shrinking bed reactors (Duff andMurray, 1996, supra; Schell et al., 2004, Bioresource Technol. 91:179-188; Lee et al., 1999, Adv. Biochem. Eng. Biotechnol. 65: 93-115).

Several methods of pretreatment under alkaline conditions can also beused. These alkaline pretreatments include, but are not limited to, limepretreatment, wet oxidation, ammonia percolation (APR), and ammoniafiber/freeze explosion (AFEX).

Lime pretreatment is performed with calcium carbonate, sodium hydroxide,or ammonia at low temperatures of 85-150° C. and residence times from 1hour to several days (Wyman et al., 2005, Bioresource Technol. 96:1959-1966; Mosier et al., 2005, Bioresource Technol. 96: 673-686). WO2006/110891, WO 2006/110899, WO 2006/110900, and WO 2006/110901 disclosepretreatment methods using ammonia.

Wet oxidation is a thermal pretreatment performed typically at 180-200°C. for 5-15 minutes with addition of an oxidative agent such as hydrogenperoxide or over-pressure of oxygen (Schmidt and Thomsen, 1998,Bioresource Technol. 64: 139-151; Palonen et al., 2004, Appl. Biochem.Biotechnol. 117: 1-17; Varga et al., 2004, Biotechnol. Bioeng. 88:567-574; Martin et al., 2006, J. Chem. Technol. Biotechnol. 81:1669-1677). The pretreatment is performed at preferably 1-40% drymatter, more preferably 2-30% dry matter, and most preferably 5-20% drymatter, and often the initial pH is increased by the addition of alkalisuch as sodium carbonate.

A modification of the wet oxidation pretreatment method, known as wetexplosion (combination of wet oxidation and steam explosion), can handledry matter up to 30%. In wet explosion, the oxidizing agent isintroduced during pretreatment after a certain residence time. Thepretreatment is then ended by flashing to atmospheric pressure (WO2006/032282).

Ammonia fiber explosion (AFEX) involves treating cellulosic materialwith liquid or gaseous ammonia at moderate temperatures such as 90-100°C. and high pressure such as 17-20 bar for 5-10 minutes, where the drymatter content can be as high as 60% (Gollapalli et al., 2002, Appl.Biochem. Biotechnol. 98: 23-35; Chundawat et al., 2007, Biotechnol.Bioeng. 96: 219-231; Alizadeh et al., 2005, Appl. Biochem. Biotechnol.121: 1133-1141; Teymouri et al., 2005, Bioresource Technol. 96:2014-2018). AFEX pretreatment results in the depolymerization ofcellulose and partial hydrolysis of hemicellulose. Lignin-carbohydratecomplexes are cleaved.

Organosolv pretreatment delignifies cellulosic material by extractionusing aqueous ethanol (40-60% ethanol) at 160-200° C. for 30-60 minutes(Pan et al., 2005, Biotechnol. Bioeng. 90: 473-481; Pan et al., 2006,Biotechnol. Bioeng. 94: 851-861; Kurabi et al., 2005, Appl. Biochem.Biotechnol. 121: 219-230). Sulphuric acid is usually added as acatalyst. In organosolv pretreatment, the majority of hemicellulose isremoved.

Other examples of suitable pretreatment methods are described by Schellet al., 2003, Appl. Biochem. and Biotechnol. 105-108: 69-85, and Mosieret al., 2005, Bioresource Technology 96: 673-686, and U.S. PublishedApplication No. 2002/0164730.

In one aspect, the chemical pretreatment is preferably carried out as anacid treatment, and more preferably as a continuous dilute and/or mildacid treatment. The acid is typically sulfuric acid, but other acids canalso be used, such as acetic acid, citric acid, nitric acid, phosphoricacid, tartaric acid, succinic acid, hydrogen chloride, or mixturesthereof. Mild acid treatment is conducted in the pH range of preferably1-5, more preferably 1-4, and most preferably 1-3. In one aspect, theacid concentration is in the range from preferably 0.01 to 20 wt % acid,more preferably 0.05 to 10 wt % acid, even more preferably 0.1 to 5 wt %acid, and most preferably 0.2 to 2.0 wt % acid. The acid is contactedwith cellulosic material and held at a temperature in the range ofpreferably 160-220° C., and more preferably 165-195° C., for periodsranging from seconds to minutes to, e.g., 1 second to 60 minutes.

In another aspect, pretreatment is carried out as an ammonia fiberexplosion step (AFEX pretreatment step).

In another aspect, pretreatment takes place in an aqueous slurry. Inpreferred aspects, cellulosic material is present during pretreatment inamounts preferably between 10-80 wt %, more preferably between 20-70 wt%, and most preferably between 30-60 wt %, such as around 50 wt %. Thepretreated cellulosic material can be unwashed or washed using anymethod known in the art, e.g., washed with water.

Mechanical Pretreatment:

The term “mechanical pretreatment” refers to various types of grindingor milling (e.g., dry milling, wet milling, or vibratory ball milling).

Physical Pretreatment:

The term “physical pretreatment” refers to any pretreatment thatpromotes the separation and/or release of cellulose, hemicellulose,and/or lignin from cellulosic material. For example, physicalpretreatment can involve irradiation (e.g., microwave irradiation),steaming/steam explosion, hydrothermolysis, and combinations thereof.

Physical pretreatment can involve high pressure and/or high temperature(steam explosion). In one aspect, high pressure means pressure in therange of preferably about 300 to about 600 psi, more preferably about350 to about 550 psi, and most preferably about 400 to about 500 psi,such as around 450 psi. In another aspect, high temperature meanstemperatures in the range of about 100 to about 300° C., preferablyabout 140 to about 235° C. In a preferred aspect, mechanicalpretreatment is performed in a batch-process, steam gun hydrolyzersystem that uses high pressure and high temperature as defined above,e.g., a Sunds Hydrolyzer available from Sunds Defibrator AB, Sweden.

Combined Physical and Chemical Pretreatment:

Cellulosic material can be pretreated both physically and chemically.For instance, the pretreatment step can involve dilute or mild acidtreatment and high temperature and/or pressure treatment. The physicaland chemical pretreatments can be carried out sequentially orsimultaneously, as desired. A mechanical pretreatment can also beincluded.

Accordingly, in a preferred aspect, cellulosic material is subjected tomechanical, chemical, or physical pretreatment, or any combinationthereof, to promote the separation and/or release of cellulose,hemicellulose, and/or lignin.

Biological Pretreatment:

The term “biological pretreatment” refers to any biological pretreatmentthat promotes the separation and/or release of cellulose, hemicellulose,and/or lignin from cellulosic material. Biological pretreatmenttechniques can involve applying lignin-solubilizing microorganisms (see,for example, Hsu, T.-A., 1996, Pretreatment of biomass, in Handbook onBioethanol: Production and Utilization, Wyman, C. E., ed., Taylor &Francis, Washington, D.C., 179-212; Ghosh and Singh, 1993,Physicochemical and biological treatments for enzymatic/microbialconversion of cellulosic biomass, Adv. Appl. Microbiol. 39: 295-333;McMillan, J. D., 1994, Pretreating lignocellulosic biomass: a review, inEnzymatic Conversion of Biomass for Fuels Production, Himmel, M. E.,Baker, J. O., and Overend, R. P., eds., ACS Symposium Series 566,American Chemical Society, Washington, D.C., chapter 15; Gong, C. S.,Cao, N. J., Du, J., and Tsao, G. T., 1999, Ethanol production fromrenewable resources, in Advances in BiochemicalEngineering/Biotechnology, Scheper, T., ed., Springer-Verlag BerlinHeidelberg, Germany, 65: 207-241; Olsson and Hahn-Hagerdal, 1996,Fermentation of lignocellulosic hydrolysates for ethanol production,Enz. Microb. Tech. 18: 312-331; and Vallander and Eriksson, 1990,Production of ethanol from lignocellulosic materials: State of the art,Adv. Biochem. Eng./Biotechnol. 42: 63-95).

Saccharification.

In the hydrolysis step, also known as saccharification, the cellulosicmaterial, e.g., pretreated, is hydrolyzed to break down cellulose andalternatively also hemicellulose to fermentable sugars, such as glucose,cellobiose, xylose, xylulose, arabinose, mannose, galactose, and/orsoluble oligosaccharides. The hydrolysis is performed enzymatically byan enzyme composition in the presence of a polypeptide havingendoglucanase activity of the present invention. The composition canfurther comprise one or more (several) hemicellulolytic or xylandegrading enzymes. The enzymes of the compositions can also be addedsequentially.

Enzymatic hydrolysis is preferably carried out in a suitable aqueousenvironment under conditions that can be readily determined by oneskilled in the art. In a preferred aspect, hydrolysis is performed underconditions suitable for the activity of the enzyme(s), i.e., optimal forthe enzyme(s). The hydrolysis can be carried out as a fed batch orcontinuous process where the pretreated cellulosic material (substrate)is fed gradually to, for example, an enzyme containing hydrolysissolution.

The saccharification is generally performed in stirred-tank reactors orfermentors under controlled pH, temperature, and mixing conditions.Suitable process time, temperature and pH conditions can readily bedetermined by one skilled in the art. For example, the saccharificationcan last up to 200 hours, but is typically performed for preferablyabout 12 to about 96 hours, more preferably about 16 to about 72 hours,and most preferably about 24 to about 48 hours. The temperature is inthe range of preferably about 25° C. to about 70° C., more preferablyabout 30° C. to about 65° C., and more preferably about 40° C. to 60°C., in particular about 50° C. The pH is in the range of preferablyabout 3 to about 8, more preferably about 3.5 to about 7, and mostpreferably about 4 to about 6, in particular about pH 5. The dry solidscontent is in the range of preferably about 5 to about 50 wt %, morepreferably about 10 to about 40 wt %, and most preferably about 20 toabout 30 wt %.

The enzyme composition preferably comprises enzymes having cellulolyticactivity and/or xylan degrading activity. In one aspect, the enzymecomposition comprises one or more (several) cellulolytic enzymes. Inanother aspect, the enzyme composition comprises one or more (several)xylan degrading enzymes. In another aspect, the enzyme compositioncomprises one or more (several) cellulolytic enzymes and one or more(several) xylan degrading enzymes.

The one or more (several) cellulolytic enzymes are preferably selectedfrom the group consisting of an endoglucanase, a cellobiohydrolase, anda beta-glucosidase. The one or more (several) xylan degrading enzymesare preferably selected from the group consisting of a xylanase, anacetyxylan esterase, a feruloyl esterase, an arabinofuranosidase, axylosidase, and a glucuronidase.

In another aspect, the enzyme composition further or even furthercomprises a polypeptide having cellulolytic enhancing activity (see, forexample, WO 2005/074647, WO 2005/074656, and WO 2007/089290). In anotheraspect, the enzyme composition may further or even further comprise oneor more (several) additional enzyme activities to improve thedegradation of the cellulose-containing material. Preferred additionalenzymes are hemicellulases (e.g., alpha-D-glucuronidases,alpha-L-arabinofuranosidases, endo-mannanases, beta-mannosidases,alpha-galactosidases, endo-alpha-L-arabinanases, beta-galactosidases),carbohydrate-esterases (e.g., acetyl-xylan esterases, acetyl-mannanesterases, ferulic acid esterases, coumaric acid esterases, glucuronoylesterases), pectinases, proteases, ligninolytic enzymes (e.g., laccases,manganese peroxidases, lignin peroxidases, H₂O₂-producing enzymes,oxidoreductases), expansins, swollenins, or mixtures thereof. In themethods of the present invention, the additional enzyme(s) can be addedprior to or during fermentation, e.g., during saccharification or duringor after propagation of the fermenting microorganism(s).

One or more (several) components of the enzyme composition may bewild-type proteins, recombinant proteins, or a combination of wild-typeproteins and recombinant proteins. For example, one or more (several)components may be native proteins of a cell, which is used as a hostcell to express recombinantly one or more (several) other components ofthe enzyme composition. One or more (several) components of the enzymecomposition may be produced as monocomponents, which are then combinedto form the enzyme composition. The enzyme composition may be acombination of multicomponent and monocomponent protein preparations.

The enzymes used in the methods of the present invention may be in anyform suitable for use in the processes described herein, such as, forexample, a crude fermentation broth with or without cells removed, acell lysate with or without cellular debris, a semi-purified or purifiedenzyme preparation, or a host cell as a source of the enzymes. Theenzyme composition may be a dry powder or granulate, a non-dustinggranulate, a liquid, a stabilized liquid, or a stabilized protectedenzyme. Liquid enzyme preparations may, for instance, be stabilized byadding stabilizers such as a sugar, a sugar alcohol or another polyol,and/or lactic acid or another organic acid according to establishedprocesses.

The optimum amounts of the enzymes and polypeptides having endoglucanaseactivity depend on several factors including, but not limited to, themixture of component cellulolytic enzymes, the cellulosic substrate, theconcentration of cellulosic substrate, the pretreatment(s) of thecellulosic substrate, temperature, time, pH, and inclusion of fermentingorganism (e.g., yeast for Simultaneous Saccharification andFermentation).

In a preferred aspect, an effective amount of cellulolytic enzyme(s) tocellulosic material is about 0.5 to about 50 mg, preferably at about 0.5to about 40 mg, more preferably at about 0.5 to about 25 mg, morepreferably at about 0.75 to about 20 mg, more preferably at about 0.75to about 15 mg, even more preferably at about 0.5 to about 10 mg, andmost preferably at about 2.5 to about 10 mg per g of cellulosicmaterial.

In another preferred aspect, an effective amount of polypeptide(s)having endoglucanase activity to cellulosic material is about 0.01 toabout 50.0 mg, preferably about 0.01 to about 40 mg, more preferablyabout 0.01 to about 30 mg, more preferably about 0.01 to about 20 mg,more preferably about 0.01 to about 10 mg, more preferably about 0.01 toabout 5 mg, more preferably at about 0.025 to about 1.5 mg, morepreferably at about 0.05 to about 1.25 mg, more preferably at about0.075 to about 1.25 mg, more preferably at about 0.1 to about 1.25 mg,even more preferably at about 0.15 to about 1.25 mg, and most preferablyat about 0.25 to about 1.0 mg per g of cellulosic material.

In another preferred aspect, an effective amount of polypeptide(s)having endoglucanase activity to cellulolytic enzyme(s) is about 0.005to about 1.0 g, preferably at about 0.01 to about 1.0 g, more preferablyat about 0.15 to about 0.75 g, more preferably at about 0.15 to about0.5 g, more preferably at about 0.1 to about 0.5 g, even more preferablyat about 0.1 to about 0.5 g, and most preferably at about 0.05 to about0.2 g per g of cellulolytic enzyme(s).

The enzymes can be derived or obtained from any suitable origin,including, bacterial, fungal, yeast, plant, or mammalian origin. Theterm “obtained” means herein that the enzyme may have been isolated froman organism that naturally produces the enzyme as a native enzyme. Theterm “obtained” also means herein that the enzyme may have been producedrecombinantly in a host organism employing methods described herein,wherein the recombinantly produced enzyme is either native or foreign tothe host organism or has a modified amino acid sequence, e.g., havingone or more (several) amino acids that are deleted, inserted and/orsubstituted, i.e., a recombinantly produced enzyme that is a mutantand/or a fragment of a native amino acid sequence or an enzyme producedby nucleic acid shuffling processes known in the art. Encompassed withinthe meaning of a native enzyme are natural variants and within themeaning of a foreign enzyme are variants obtained recombinantly, such asby site-directed mutagenesis or shuffling.

A polypeptide having cellulolytic enzyme activity or xylan degradingactivity may be a bacterial polypeptide. For example, the polypeptidemay be a gram positive bacterial polypeptide such as a Bacillus,Streptococcus, Streptomyces, Staphylococcus, Enterococcus,Lactobacillus, Lactococcus, Clostridium, Geobacillus, or Oceanobacilluspolypeptide having cellulolytic enzyme activity or xylan degradingactivity, or a Gram negative bacterial polypeptide such as an E. coli,Pseudomonas, Salmonella, Campylobacter, Helicobacter, Flavobacterium,Fusobacterium, Ilyobacter, Neisseria, or Ureaplasma polypeptide havingcellulolytic enzyme activity or xylan degrading activity.

In a preferred aspect, the polypeptide is a Bacillus alkalophilus,Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans,Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus,Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacilluspumilus, Bacillus stearothermophilus, Bacillus subtilis, or Bacillusthuringiensis polypeptide having cellulolytic enzyme activity or xylandegrading activity.

In another preferred aspect, the polypeptide is a Streptococcusequisimilis, Streptococcus pyogenes, Streptococcus uberis, orStreptococcus equi subsp. Zooepidemicus polypeptide having cellulolyticenzyme activity or xylan degrading activity.

In another preferred aspect, the polypeptide is a Streptomycesachromogenes, Streptomyces avermitilis, Streptomyces coelicolor,Streptomyces griseus, or Streptomyces lividans polypeptide havingcellulolytic enzyme activity or xylan degrading activity.

The polypeptide having cellulolytic enzyme activity or xylan degradingactivity may also be a fungal polypeptide, and more preferably a yeastpolypeptide such as a Candida, Kluyveromyces, Pichia, Saccharomyces,Schizosaccharomyces, or Yarrowia polypeptide having cellulolytic enzymeactivity or xylan degrading activity; or more preferably a filamentousfungal polypeptide such as an Acremonium, Agaricus, Alternaria,Aspergillus, Aureobasidium, Botryospaeria, Ceriporiopsis, Chaetomidium,Chrysosporium, Claviceps, Cochliobolus, Coprinopsis, Coptotermes,Corynascus, Cryphonectria, Cryptococcus, Diplodia, Exidia, Filibasidium,Fusarium, Gibberella, Holomastigotoides, Humicola, Irpex, Lentinula,Leptospaeria, Magnaporthe, Melanocarpus, Meripilus, Mucor,Myceliophthora, Neocallimastix, Neurospora, Paecilomyces, Penicillium,Phanerochaete, Piromyces, Poitrasia, Pseudoplectania,Pseudotrichonympha, Rhizomucor, Schizophyllum, Scytalidium, Talaromyces,Thermoascus, Thielavia, Tolypocladium, Trichoderma, Trichophaea,Verticillium, Volvariella, or Xylaria polypeptide having cellulolyticenzyme activity or xylan degrading activity.

In a preferred aspect, the polypeptide is a Saccharomycescarlsbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus,Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomycesnorbensis, or Saccharomyces oviformis polypeptide having cellulolyticenzyme activity or xylan degrading activity.

In another preferred aspect, the polypeptide is an Acremoniumcellulolyticus, Aspergillus aculeatus, Aspergillus awamori, Aspergillusfumigatus, Aspergillus foetidus, Aspergillus japonicus, Aspergillusnidulans, Aspergillus niger, Aspergillus oryzae, Chrysosporiumkeratinophilum, Chrysosporium lucknowense, Chrysosporium tropicum,Chrysosporium merdarium, Chrysosporium inops, Chrysosporium pannicola,Chrysosporium queenslandicum, Chrysosporium zonatum, Fusariumbactridioides, Fusarium cerealis, Fusarium crookwellense, Fusariumculmorum, Fusarium graminearum, Fusarium graminum, Fusariumheterosporum, Fusarium negundi, Fusarium oxysporum, Fusariumreticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum,Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulosum,Fusarium trichothecioides, Fusarium venenatum, Humicola grisea, Humicolainsolens, Humicola lanuginosa, Irpex lacteus, Mucor miehei,Myceliophthora thermophila, Neurospora crassa, Penicillium funiculosum,Penicillium purpurogenum, Phanerochaete chrysosporium, Thielaviaachromatica, Thielavia albomyces, Thielavia albopilosa, Thielaviaaustraleinsis, Thielavia fimeti, Thielavia microspora, Thielaviaovispora, Thielavia peruviana, Thielavia spededonium, Thielavia setosa,Thielavia sub thermophila, Thielavia terrestris, Trichoderma harzianum,Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei,Trichoderma viride, or Trichophaea saccata polypeptide havingcellulolytic enzyme activity or xylan degrading activity.

Chemically modified or protein engineered mutants of polypeptides havingcellulolytic enzyme activity or xylan degrading activity may also beused.

One or more (several) components of the enzyme composition may be arecombinant component, i.e., produced by cloning of a DNA sequenceencoding the single component and subsequent cell transformed with theDNA sequence and expressed in a host (see, for example, WO 91/17243 andWO 91/17244). The host is preferably a heterologous host (enzyme isforeign to host), but the host may under certain conditions also be ahomologous host (enzyme is native to host). Monocomponent cellulolyticproteins may also be prepared by purifying such a protein from afermentation broth.

Examples of commercial cellulolytic protein preparations suitable foruse in the present invention include, for example, CELLIC™ Ctec(Novozymes A/S), CELLUCLAST™ (Novozymes A/S), NOVOZYM™ 188 (NovozymesA/S), CELLUZYME™ (Novozymes A/S), CEREFLO™ (Novozymes A/S), andULTRAFLO™ (Novozymes A/S), ACCELERASE™ (Genencor Int.), LAMINEX™(Genencor Int.), SPEZYME™ CP (Genencor Int.), ROHAMENT™ 7069 W (RöhmGmbH), FIBREZYME® LDI (Dyadic International, Inc.), FIBREZYME® LBR(Dyadic International, Inc.), or VISCOSTAR® 150L (Dyadic International,Inc.). The cellulase enzymes are added in amounts effective from about0.001 to about 5.0 wt % of solids, more preferably from about 0.025 toabout 4.0 wt % of solids, and most preferably from about 0.005 to about2.0 wt % of solids. The cellulase enzymes are added in amounts effectivefrom about 0.001 to about 5.0 wt % of solids, more preferably from about0.025 to about 4.0 wt % of solids, and most preferably from about 0.005to about 2.0 wt % of solids.

Examples of bacterial endoglucanases that can be used in the methods ofthe present invention as an additional endoglucanase, include, but arenot limited to, an Acidothermus cellulolyticus endoglucanase (WO91/05039; WO 93/15186; U.S. Pat. No. 5,275,944; WO 96/02551; U.S. Pat.No. 5,536,655, WO 00/70031, WO 05/093050); Thermobifida fuscaendoglucanase III (WO 05/093050); and Thermobifida fusca endoglucanase V(WO 05/093050).

Examples of fungal endoglucanases that can be used as an additionalendoglucanase in the methods of the present invention, include, but arenot limited to, a Trichoderma reesei endoglucanase I (Penttila et al.,1986, Gene 45: 253-263; GENBANK™ accession no. M15665); Trichodermareesei endoglucanase II (Saloheimo, et al., 1988, Gene 63:11-22;GENBANK™ accession no. M19373); Trichoderma reesei endoglucanase III(Okada et al., 1988, Appl. Environ. Microbiol. 64: 555-563; GENBANK™accession no. AB003694); and Trichoderma reesei endoglucanase V(Saloheimo et al., 1994, Molecular Microbiology 13: 219-228; GENBANK™accession no. Z33381); Aspergillus aculeatus endoglucanase (Ooi et al.,1990, Nucleic Acids Research 18: 5884); Aspergillus kawachiiendoglucanase (Sakamoto et al., 1995, Current Genetics 27: 435-439);Erwinia carotovara endoglucanase (Saarilahti et al., 1990, Gene 90:9-14); Fusarium oxysporum endoglucanase (GENBANK™ accession no. L29381);Humicola grisea var. thermoidea endoglucanase (GENBANK™ accession no.AB003107); Melanocarpus albomyces endoglucanase (GENBANK™ accession no.MAL515703); Neurospora crassa endoglucanase (GENBANK™ accession no.XM_(—)324477); Humicola insolens endoglucanase V; Myceliophthorathermophila CBS 117.65 endoglucanase; basidiomycete CBS 495.95endoglucanase; basidiomycete CBS 494.95 endoglucanase; Thielaviaterrestris NRRL 8126 CEL6B endoglucanase; Thielavia terrestris NRRL 8126CEL6C endoglucanase); Thielavia terrestris NRRL 8126 CEL7Cendoglucanase; Thielavia terrestris NRRL 8126 CEL7E endoglucanase;Thielavia terrestris NRRL 8126 CEL7F endoglucanase; Cladorrhinumfoecundissimum ATCC 62373 CEL7A endoglucanase; and Trichoderma reeseistrain No. VTT-D-80133 endoglucanase (GENBANK™ accession no. M15665).

Examples of cellobiohydrolases useful in the methods of the presentinvention include, but are not limited to, Trichoderma reeseicellobiohydrolase I; Trichoderma reesei cellobiohydrolase II; Humicolainsolens cellobiohydrolase I, Myceliophthora thermophilacellobiohydrolase II, Thielavia terrestris cellobiohydrolase II (CEL6A),Chaetomium thermophilum cellobiohydrolase I, and Chaetomium thermophilumcellobiohydrolase II.

Examples of beta-glucosidases useful in the methods of the presentinvention include, but are not limited to, Aspergillus oryzaebeta-glucosidase; Aspergillus fumigatus beta-glucosidase; Penicilliumbrasilianum IBT 20888 beta-glucosidase; Aspergillus nigerbeta-glucosidase; and Aspergillus aculeatus beta-glucosidase.

The Aspergillus oryzae polypeptide having beta-glucosidase activity canbe obtained according to WO 2002/095014. The Aspergillus fumigatuspolypeptide having beta-glucosidase activity can be obtained accordingto WO 2005/047499. The Penicillium brasilianum polypeptide havingbeta-glucosidase activity can be obtained according to WO 2007/019442.The Aspergillus niger polypeptide having beta-glucosidase activity canbe obtained according to Dan et al., 2000, J. Biol. Chem. 275:4973-4980. The Aspergillus aculeatus polypeptide having beta-glucosidaseactivity can be obtained according to Kawaguchi et al., 1996, Gene 173:287-288.

The beta-glucosidase may be a fusion protein. In one aspect, thebeta-glucosidase is the Aspergillus oryzae beta-glucosidase variant BGfusion protein or the Aspergillus oryzae beta-glucosidase fusion proteinobtained according to WO 2008/057637.

Other endoglucanases, cellobiohydrolases, and beta-glucosidases aredisclosed in numerous Glycosyl Hydrolase families using theclassification according to Henrissat, 1991, A classification ofglycosyl hydrolases based on amino-acid sequence similarities, Biochem.J. 280: 309-316, and Henrissat and Bairoch, 1996, Updating thesequence-based classification of glycosyl hydrolases, Biochem. J. 316:695-696.

Other cellulolytic enzymes that may be used in the present invention aredescribed in EP 495,257, EP 531,315, EP 531,372, WO 89/09259, WO94/07998, WO 95/24471, WO 96/11262, WO 96/29397, WO 96/034108, WO97/14804, WO 98/08940, WO 98/012307, WO 98/13465, WO 98/015619, WO98/015633, WO 98/028411, WO 99/06574, WO 99/10481, WO 99/025846, WO99/025847, WO 99/031255, WO 2000/009707, WO 2002/050245, WO2002/0076792, WO 2002/101078, WO 2003/027306, WO 2003/052054, WO2003/052055, WO 2003/052056, WO 2003/052057, WO 2003/052118, WO2004/016760, WO 2004/043980, WO 2004/048592, WO 2005/001065, WO2005/028636, WO 2005/093050, WO 2005/093073, WO 2006/074005, WO2006/117432, WO 2007/071818, WO 2007/071820, WO 2008/008070, WO2008/008793, U.S. Pat. No. 4,435,307, U.S. Pat. No. 5,457,046, U.S. Pat.No. 5,648,263, U.S. Pat. No. 5,686,593, U.S. Pat. No. 5,691,178, U.S.Pat. No. 5,763,254, and U.S. Pat. No. 5,776,757.

In the methods of the present invention, any GH61 polypeptide havingcellulolytic enhancing activity can be used.

Examples of polypeptides having cellulolytic enhancing activity usefulin the methods of the present invention include, but are not limited to,polypeptides having cellulolytic enhancing activity from Thielaviaterrestris (WO 2005/074647); polypeptides having cellulolytic enhancingactivity from Thermoascus aurantiacus (WO 2005/074656); polypeptideshaving cellulolytic enhancing activity from Trichoderma reesei (WO2007/089290); and polypeptides having cellulolytic enhancing activityfrom Myceliophthora thermophila (WO 2009/085935; WO 2009/085859; WO2009/085864; WO 2009/085868).

Examples of commercial xylan degrading enzyme preparations suitable foruse in the present invention include, for example, SHEARZYME™ (NovozymesA/S), CELLIC™ Htec (Novozymes A/S), VISCOZYME® (Novozymes A/S),ULTRAFLO® (Novozymes A/S), PULPZYME® HC (Novozymes A/S), MULTIFECT®Xylanase (Genencor), ECOPULP® TX-200A (AB Enzymes), HSP 6000 Xylanase(DSM), DEPOL™ 333P (Biocatalysts Limit, Wales, UK), DEPOL™ 740L.(Biocatalysts Limit, Wales, UK), and DEPOL™ 762P (Biocatalysts Limit,Wales, UK).

Examples of xylanases useful in the methods of the present inventioninclude, but are not limited to, Aspergillus aculeatus xylanase(GeneSeqP:AAR63790; WO 94/21785), Aspergillus fumigatus xylanases (WO2006/078256), and Thielavia terrestris NRRL 8126 xylanases (WO2009/079210).

Examples of beta-xylosidases useful in the methods of the presentinvention include, but are not limited to, Trichoderma reeseibeta-xylosidase (UniProtKB/TrEMBL accession number 092458), Talaromycesemersonii (SwissProt accession number Q8×212), and Neurospora crassa(SwissProt accession number Q7SOW4).

Examples of acetylxylan esterases useful in the methods of the presentinvention include, but are not limited to, Hypocrea jecorina acetylxylanesterase (WO 2005/001036), Neurospora crassa acetylxylan esterase(UniProt accession number q7s259), Thielavia terrestris NRRL 8126acetylxylan esterase (WO 2009/042846), Chaetomium globosum acetylxylanesterase (Uniprot accession number Q2GWX4), Chaetomium gracileacetylxylan esterase (GeneSeqP accession number AAB82124), Phaeosphaerianodorum acetylxylan esterase (Uniprot accession number QOUHJ1), andHumicola insolens DSM 1800 acetylxylan esterase (WO 2009/073709).

Examples of ferulic acid esterases useful in the methods of the presentinvention include, but are not limited to, Humicola insolens DSM 1800feruloyl esterase (WO 2009/076122), Neurospora crassa feruloyl esterase(UniProt accession number Q9HGR3), and Neosartorya fischeri feruloylesterase (UniProt Accession number A1D9T4).

Examples of arabinofuranosidases useful in the methods of the presentinvention include, but are not limited to, Humicola insolens DSM 1800arabinofuranosidase (WO 2009/073383) and Aspergillus nigerarabinofuranosidase (GeneSeqP accession number AAR94170).

Examples of alpha-glucuronidases useful in the methods of the presentinvention include, but are not limited to, Aspergillus clavatusalpha-glucuronidase (UniProt accession number alcc12), Trichodermareesei alpha-glucuronidase (Uniprot accession number Q99024),Talaromyces emersonii alpha-glucuronidase (UniProt accession numberQ8×211), Aspergillus niger alpha-glucuronidase (Uniprot accession numberQ96WX9), Aspergillus terreus alpha-glucuronidase (SwissProt accessionnumber Q0CJP9), and Aspergillus fumigatus alpha-glucuronidase (SwissProtaccession number Q4WW45).

The enzymes and proteins used in the methods of the present inventionmay be produced by fermentation of the above-noted microbial strains ona nutrient medium containing suitable carbon and nitrogen sources andinorganic salts, using procedures known in the art (see, e.g., Bennett,J. W. and LaSure, L. (eds.), More Gene Manipulations in Fungi, AcademicPress, CA, 1991). Suitable media are available from commercial suppliersor may be prepared according to published compositions (e.g., incatalogues of the American Type Culture Collection). Temperature rangesand other conditions suitable for growth and enzyme production are knownin the art (see, e.g., Bailey, J. E., and 011 is, D. F., BiochemicalEngineering Fundamentals, McGraw-Hill Book Company, NY, 1986).

The fermentation can be any method of cultivation of a cell resulting inthe expression or isolation of an enzyme. Fermentation may, therefore,be understood as comprising shake flask cultivation, or small- orlarge-scale fermentation (including continuous, batch, fed-batch, orsolid state fermentations) in laboratory or industrial fermentorsperformed in a suitable medium and under conditions allowing the enzymeto be expressed or isolated. The resulting enzymes produced by themethods described above may be recovered from the fermentation mediumand purified by conventional procedures.

Fermentation.

The fermentable sugars obtained from the hydrolyzed cellulosic materialcan be fermented by one or more (several) fermenting microorganismscapable of fermenting the sugars directly or indirectly into a desiredfermentation product. “Fermentation” or “fermentation process” refers toany fermentation process or any process comprising a fermentation step.Fermentation processes also include fermentation processes used in theconsumable alcohol industry (e.g., beer and wine), dairy industry (e.g.,fermented dairy products), leather industry, and tobacco industry. Thefermentation conditions depend on the desired fermentation product andfermenting organism and can easily be determined by one skilled in theart.

In the fermentation step, sugars, released from cellulosic material as aresult of the pretreatment and enzymatic hydrolysis steps, are fermentedto a product, e.g., ethanol, by a fermenting organism, such as yeast.Hydrolysis (saccharification) and fermentation can be separate orsimultaneous, as described herein.

Any suitable hydrolyzed cellulosic material can be used in thefermentation step in practicing the present invention. The material isgenerally selected based on the desired fermentation product, i.e., thesubstance to be obtained from the fermentation, and the processemployed, as is well known in the art.

The term “fermentation medium” is understood herein to refer to a mediumbefore the fermenting microorganism(s) is(are) added, such as, a mediumresulting from a saccharification process, as well as a medium used in asimultaneous saccharification and fermentation process (SSF).

“Fermenting microorganism” refers to any microorganism, includingbacterial and fungal organisms, suitable for use in a desiredfermentation process to produce a fermentation product. The fermentingorganism can be C₆ and/or C₅ fermenting organisms, or a combinationthereof. Both C₆ and C₅ fermenting organisms are well known in the art.Suitable fermenting microorganisms are able to ferment, i.e., convert,sugars, such as glucose, xylose, xylulose, arabinose, maltose, mannose,galactose, or oligosaccharides, directly or indirectly into the desiredfermentation product.

Examples of bacterial and fungal fermenting organisms producing ethanolare described by Lin et al., 2006, Appl. Microbiol. Biotechnol. 69:627-642.

Examples of fermenting microorganisms that can ferment C₆ sugars includebacterial and fungal organisms, such as yeast. Preferred yeast includesstrains of the Saccharomyces spp., preferably Saccharomyces cerevisiae.

Examples of fermenting organisms that can ferment C₅ sugars includebacterial and fungal organisms, such as yeast. Preferred C₅ fermentingyeast include strains of Pichia, preferably Pichia stipitis, such asPichia stipitis CBS 5773; strains of Candida, preferably Candidaboidinii, Candida brassicae, Candida sheatae, Candida diddensii, Candidapseudotropicalis, or Candida utilis.

Other fermenting organisms include strains of Zymomonas, such asZymomonas mobilis; Hansenula, such as Hansenula anomala; Kluyveromyces,such as K. fragilis; Schizosaccharomyces, such as S. pombe; and E. coli,especially E. coli strains that have been genetically modified toimprove the yield of ethanol.

In a preferred aspect, the yeast is a Saccharomyces spp. In a morepreferred aspect, the yeast is Saccharomyces cerevisiae. In another morepreferred aspect, the yeast is Saccharomyces distaticus. In another morepreferred aspect, the yeast is Saccharomyces uvarum. In anotherpreferred aspect, the yeast is a Kluyveromyces. In another morepreferred aspect, the yeast is Kluyveromyces marxianus. In another morepreferred aspect, the yeast is Kluyveromyces fragilis. In anotherpreferred aspect, the yeast is a Candida. In another more preferredaspect, the yeast is Candida boidinii. In another more preferred aspect,the yeast is Candida brassicae. In another more preferred aspect, theyeast is Candida diddensii. In another more preferred aspect, the yeastis Candida pseudotropicalis. In another more preferred aspect, the yeastis Candida utilis. In another preferred aspect, the yeast is aClavispora. In another more preferred aspect, the yeast is Clavisporalusitaniae. In another more preferred aspect, the yeast is Clavisporaopuntiae. In another preferred aspect, the yeast is a Pachysolen. Inanother more preferred aspect, the yeast is Pachysolen tannophilus. Inanother preferred aspect, the yeast is a Pichia. In another morepreferred aspect, the yeast is a Pichia stipitis. In another preferredaspect, the yeast is a Bretannomyces. In another more preferred aspect,the yeast is Bretannomyces clausenii (Philippidis, G. P., 1996,Cellulose bioconversion technology, in Handbook on Bioethanol:Production and Utilization, Wyman, C. E., ed., Taylor & Francis,Washington, D.C., 179-212).

Bacteria that can efficiently ferment hexose and pentose to ethanolinclude, for example, Zymomonas mobilis and Clostridium thermocellum(Philippidis, 1996, supra).

In a preferred aspect, the bacterium is a Zymomonas. In a more preferredaspect, the bacterium is Zymomonas mobilis. In another preferred aspect,the bacterium is a Clostridium. In another more preferred aspect, thebacterium is Clostridium thermocellum.

Commercially available yeast suitable for ethanol production includes,e.g., ETHANOL RED™ yeast (available from Fermentis/Lesaffre, USA), FALI™(available from Fleischmann's Yeast, USA), SUPERSTART™ and THERMOSACC™fresh yeast (available from Ethanol Technology, WI, USA), BIOFERM™ AFTand XR (available from NABC—North American Bioproducts Corporation, GA,USA), GERT STRAND™ (available from Gert Strand AB, Sweden), and FERMIOL™(available from DSM Specialties).

In a preferred aspect, the fermenting microorganism has been geneticallymodified to provide the ability to ferment pentose sugars, such asxylose utilizing, arabinose utilizing, and xylose and arabinoseco-utilizing microorganisms.

The cloning of heterologous genes into various fermenting microorganismshas led to the construction of organisms capable of converting hexosesand pentoses to ethanol (cofermentation) (Chen and Ho, 1993, Cloning andimproving the expression of Pichia stipitis xylose reductase gene inSaccharomyces cerevisiae, Appl. Biochem. Biotechnol. 39-40: 135-147; Hoet al., 1998, Genetically engineered Saccharomyces yeast capable ofeffectively cofermenting glucose and xylose, Appl. Environ. Microbiol.64: 1852-1859; Kotter and Ciriacy, 1993, Xylose fermentation bySaccharomyces cerevisiae, Appl. Microbiol. Biotechnol. 38: 776-783;Walfridsson et al., 1995, Xylose-metabolizing Saccharomyces cerevisiaestrains overexpressing the TKL1 and TAL1 genes encoding the pentosephosphate pathway enzymes transketolase and transaldolase, Appl.Environ. Microbiol. 61: 4184-4190; Kuyper et al., 2004, Minimalmetabolic engineering of Saccharomyces cerevisiae for efficientanaerobic xylose fermentation: a proof of principle, FEMS Yeast Research4: 655-664; Beall et al., 1991, Parametric studies of ethanol productionfrom xylose and other sugars by recombinant Escherichia coli, Biotech.Bioeng. 38: 296-303; Ingram et al., 1998, Metabolic engineering ofbacteria for ethanol production, Biotechnol. Bioeng. 58: 204-214; Zhanget al., 1995, Metabolic engineering of a pentose metabolism pathway inethanologenic Zymomonas mobilis, Science 267: 240-243; Deanda et al.,1996, Development of an arabinose-fermenting Zymomonas mobilis strain bymetabolic pathway engineering, Appl. Environ. Microbiol. 62: 4465-4470;WO 2003/062430, xylose isomerase).

In a preferred aspect, the genetically modified fermenting microorganismis Saccharomyces cerevisiae. In another preferred aspect, thegenetically modified fermenting microorganism is Zymomonas mobilis. Inanother preferred aspect, the genetically modified fermentingmicroorganism is Escherichia coli. In another preferred aspect, thegenetically modified fermenting microorganism is Klebsiella oxytoca. Inanother preferred aspect, the genetically modified fermentingmicroorganism is Kluyveromyces sp.

It is well known in the art that the organisms described above can alsobe used to produce other substances, as described herein.

The fermenting microorganism is typically added to the degradedlignocellulose or hydrolysate and the fermentation is performed forabout 8 to about 96 hours, such as about 24 to about 60 hours. Thetemperature is typically between about 26° C. to about 60° C., inparticular about 32° C. or 50° C., and at about pH 3 to about pH 8, suchas around pH 4-5, 6, or 7.

In a preferred aspect, the yeast and/or another microorganism is appliedto the degraded cellulosic material and the fermentation is performedfor about 12 to about 96 hours, such as typically 24-60 hours. In apreferred aspect, the temperature is preferably between about 20° C. toabout 60° C., more preferably about 25° C. to about 50° C., and mostpreferably about 32° C. to about 50° C., in particular about 32° C. or50° C., and the pH is generally from about pH 3 to about pH 7,preferably around pH 4-7. However, some fermenting organisms, e.g.,bacteria, have higher fermentation temperature optima. Yeast or anothermicroorganism is preferably applied in amounts of approximately 10⁵ to10¹², preferably from approximately 10⁷ to 10¹⁰, especiallyapproximately 2×10⁸ viable cell count per ml of fermentation broth.Further guidance in respect of using yeast for fermentation can be foundin, e.g., “The Alcohol Textbook” (Editors K. Jacques, T. P. Lyons and D.R. Kelsall, Nottingham University Press, United Kingdom 1999), which ishereby incorporated by reference.

For ethanol production, following the fermentation the fermented slurryis distilled to extract the ethanol. The ethanol obtained according tothe methods of the invention can be used as, e.g., fuel ethanol,drinking ethanol, i.e., potable neutral spirits, or industrial ethanol.

A fermentation stimulator can be used in combination with any of theprocesses described herein to further improve the fermentation process,and in particular, the performance of the fermenting microorganism, suchas, rate enhancement and ethanol yield. A “fermentation stimulator”refers to stimulators for growth of the fermenting microorganisms, inparticular, yeast. Preferred fermentation stimulators for growth includevitamins and minerals. Examples of vitamins include multivitamins,biotin, pantothenate, nicotinic acid, meso-inositol, thiamine,pyridoxine, para-aminobenzoic acid, folic acid, riboflavin, and VitaminsA, B, C, D, and E. See, for example, Alfenore et al., Improving ethanolproduction and viability of Saccharomyces cerevisiae by a vitaminfeeding strategy during fed-batch process, Springer-Verlag (2002), whichis hereby incorporated by reference. Examples of minerals includeminerals and mineral salts that can supply nutrients comprising P, K,Mg, S, Ca, Fe, Zn, Mn, and Cu.

Fermentation Products:

A fermentation product can be any substance derived from thefermentation. The fermentation product can be, without limitation, analcohol (e.g., arabinitol, butanol, ethanol, glycerol, methanol,1,3-propanediol, sorbitol, and xylitol); an organic acid (e.g., aceticacid, acetonic acid, adipic acid, ascorbic acid, citric acid,2,5-diketo-D-gluconic acid, formic acid, fumaric acid, glucaric acid,gluconic acid, glucuronic acid, glutaric acid, 3-hydroxypropionic acid,itaconic acid, lactic acid, malic acid, malonic acid, oxalic acid,oxaloacetic acid, propionic acid, succinic acid, and xylonic acid); aketone (e.g., acetone); an amino acid (e.g., aspartic acid, glutamicacid, glycine, lysine, serine, and threonine); and a gas (e.g., methane,hydrogen (H₂), carbon dioxide (CO₂), and carbon monoxide (CO)). Thefermentation product can also be protein as a high value product.

In a preferred aspect, the fermentation product is an alcohol. It willbe understood that the term “alcohol” encompasses a substance thatcontains one or more hydroxyl moieties. In a more preferred aspect, thealcohol is arabinitol. In another more preferred aspect, the alcohol isbutanol. In another more preferred aspect, the alcohol is ethanol. Inanother more preferred aspect, the alcohol is glycerol. In another morepreferred aspect, the alcohol is methanol. In another more preferredaspect, the alcohol is 1,3-propanediol. In another more preferredaspect, the alcohol is sorbitol. In another more preferred aspect, thealcohol is xylitol. See, for example, Gong, C. S., Cao, N. J., Du, J.,and Tsao, G. T., 1999, Ethanol production from renewable resources, inAdvances in Biochemical Engineering/Biotechnology, Scheper, T., ed.,Springer-Verlag Berlin Heidelberg, Germany, 65: 207-241; Silveira andJonas, 2002, The biotechnological production of sorbitol, Appl.Microbiol. Biotechnol. 59: 400-408; Nigam and Singh, 1995, Processes forfermentative production of xylitol—a sugar substitute, ProcessBiochemistry 30(2): 117-124; Ezeji et al., 2003, Production of acetone,butanol and ethanol by Clostridium beijerinckii BA101 and in siturecovery by gas stripping, World Journal of Microbiology andBiotechnology 19 (6): 595-603.

In another preferred aspect, the fermentation product is an organicacid. In another more preferred aspect, the organic acid is acetic acid.In another more preferred aspect, the organic acid is acetonic acid. Inanother more preferred aspect, the organic acid is adipic acid. Inanother more preferred aspect, the organic acid is ascorbic acid. Inanother more preferred aspect, the organic acid is citric acid. Inanother more preferred aspect, the organic acid is 2,5-diketo-D-gluconicacid. In another more preferred aspect, the organic acid is formic acid.In another more preferred aspect, the organic acid is fumaric acid. Inanother more preferred aspect, the organic acid is glucaric acid. Inanother more preferred aspect, the organic acid is gluconic acid. Inanother more preferred aspect, the organic acid is glucuronic acid. Inanother more preferred aspect, the organic acid is glutaric acid. Inanother preferred aspect, the organic acid is 3-hydroxypropionic acid.In another more preferred aspect, the organic acid is itaconic acid. Inanother more preferred aspect, the organic acid is lactic acid. Inanother more preferred aspect, the organic acid is malic acid. Inanother more preferred aspect, the organic acid is malonic acid. Inanother more preferred aspect, the organic acid is oxalic acid. Inanother more preferred aspect, the organic acid is propionic acid. Inanother more preferred aspect, the organic acid is succinic acid. Inanother more preferred aspect, the organic acid is xylonic acid. See,for example, Chen and Lee, 1997, Membrane-mediated extractivefermentation for lactic acid production from cellulosic biomass, Appl.Biochem. Biotechnol. 63-65: 435-448.

In another preferred aspect, the fermentation product is a ketone. Itwill be understood that the term “ketone” encompasses a substance thatcontains one or more ketone moieties. In another more preferred aspect,the ketone is acetone. See, for example, Qureshi and Blaschek, 2003,supra.

In another preferred aspect, the fermentation product is an amino acid.In another more preferred aspect, the organic acid is aspartic acid. Inanother more preferred aspect, the amino acid is glutamic acid. Inanother more preferred aspect, the amino acid is glycine. In anothermore preferred aspect, the amino acid is lysine. In another morepreferred aspect, the amino acid is serine. In another more preferredaspect, the amino acid is threonine. See, for example, Richard andMargaritis, 2004, Empirical modeling of batch fermentation kinetics forpoly(glutamic acid) production and other microbial biopolymers,Biotechnology and Bioengineering 87(4): 501-515.

In another preferred aspect, the fermentation product is a gas. Inanother more preferred aspect, the gas is methane. In another morepreferred aspect, the gas is H₂. In another more preferred aspect, thegas is CO₂. In another more preferred aspect, the gas is CO. See, forexample, Kataoka, N., A. Miya, and K. Kiriyama, 1997, Studies onhydrogen production by continuous culture system of hydrogen-producinganaerobic bacteria, Water Science and Technology 36(6-7): 41-47; andGunaseelan, 1997, Biomass and Bioenergy 13(1-2): 83-114, Anaerobicdigestion of biomass for methane production: A review.

Recovery.

The fermentation product(s) can be optionally recovered from thefermentation medium using any method known in the art including, but notlimited to, chromatography, electrophoretic procedures, differentialsolubility, distillation, or extraction. For example, alcohol isseparated from the fermented cellulosic material and purified byconventional methods of distillation. Ethanol with a purity of up toabout 96 vol. % can be obtained, which can be used as, for example, fuelethanol, drinking ethanol, i.e., potable neutral spirits, or industrialethanol.

Signal Peptide and Propeptide

The present invention also relates to an isolated polynucleotideencoding a signal peptide comprising or consisting of amino acids 1 to18 of SEQ ID NO: 2. The present invention also relates to an isolatedpolynucleotide encoding a signal peptide and a propeptide comprising orconsisting of amino acids 1 to 18 of SEQ ID NO: 2. The polynucleotidesmay further comprise a gene encoding a protein, which is operably linkedto the signal peptide and/or propeptide. The protein is preferablyforeign to the signal peptide and/or propeptide. In one aspect, thepolynucleotide encoding the signal peptide is nucleotides 1 to 54 of SEQID NO: 1.

The present invention also relates to nucleic acid constructs,expression vectors and recombinant host cells comprising suchpolynucleotides.

The present invention also relates to methods of producing a protein,comprising (a) cultivating a recombinant host cell comprising suchpolynucleotide; and (b) recovering the protein.

The protein may be native or heterologous to a host cell. The term“protein” is not meant herein to refer to a specific length of theencoded product and, therefore, encompasses peptides, oligopeptides, andpolypeptides. The term “protein” also encompasses two or morepolypeptides combined to form the encoded product. The proteins alsoinclude hybrid polypeptides and fused polypeptides.

Preferably, the protein is a hormone, enzyme, receptor or portionthereof, antibody or portion thereof, or reporter. For example, theprotein may be a hydrolase, isomerase, ligase, lyase, oxidoreductase, ortransferase, e.g., an aminopeptidase, amylase, carbohydrase,carboxypeptidase, catalase, cellobiohydrolase, cellulase, chitinase,cutinase, cyclodextrin glycosyltransferase, deoxyribonuclease,endoglucanase, esterase, alpha-galactosidase, beta-galactosidase,glucoamylase, alpha-glucosidase, beta-glucosidase, invertase, laccase,lipase, mannosidase, mutanase, oxidase, pectinolytic enzyme, peroxidase,phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease,transglutaminase, xylanase, or beta-xylosidase.

The gene may be obtained from any prokaryotic, eukaryotic, or othersource.

The present invention is further described by the following examplesthat should not be construed as limiting the scope of the invention.

LIST OF PREFERRED EMBODIMENTS Embodiment 1

An isolated polypeptide having endoglucanase activity, selected from thegroup consisting of:

(a) a polypeptide having at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the mature polypeptide of SEQ ID NO: 2;

(b) a polypeptide encoded by a polynucleotide that hybridizes undermedium-high stringency conditions, high stringency conditions, or veryhigh stringency conditions with (i) the mature polypeptide codingsequence of SEQ ID NO: 1, or (ii) the full-length complement of (i);

(c) a polypeptide encoded by a polynucleotide having at least 75%, atleast 80%, at least 85%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the maturepolypeptide coding sequence of SEQ ID NO: 1;

(d) a variant of the mature polypeptide of SEQ ID NO: 2 comprising asubstitution, deletion, and/or insertion at one or several positions;and (e) a fragment of the polypeptide of (a), (b), (c), or (d) that hasendoglucanase activity.

Embodiment 2

The polypeptide of embodiment 1, having at least 75%, at least 80%, atleast 85%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99% or 100% sequence identity to the mature polypeptide of SEQ IDNO: 2.

Embodiment 3

The polypeptide of embodiment 1 or 2, which is encoded by apolynucleotide that hybridizes under medium-high stringency conditions,high stringency conditions, or very high stringency conditions with (i)the mature polypeptide coding sequence of SEQ ID NO: 1, or (ii) thefull-length complement of (i).

Embodiment 4

The polypeptide of any of embodiments 1-3, which is encoded by apolynucleotide having at least 75%, at least 80%, at least 85%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, at least 99% or 100%sequence identity to the mature polypeptide coding sequence of SEQ IDNO: 1.

Embodiment 5

The polypeptide of any of embodiments 1-4, comprising or consisting ofSEQ ID NO: 2 or the mature polypeptide of SEQ ID NO: 2.

Embodiment 6

The polypeptide of embodiment 5, wherein the mature polypeptide is aminoacids 19 to 477 of SEQ ID NO: 2.

Embodiment 7

An isolated polypeptide comprising a catalytic domain selected from thegroup consisting of:

(a) a catalytic domain having at least 80% sequence identity to aminoacids 19 to 397 of SEQ ID NO: 2;

(b) a catalytic domain encoded by a polynucleotide that hybridizes underhigh, or very high stringency conditions with (i) nucleotides 55 to 1191of SEQ ID NO: 1, or (ii) the full-length complement of (i);

(c) a catalytic domain encoded by a polynucleotide having at least 80%sequence identity to the catalytic domain of SEQ ID NO: 1;

(d) a variant of amino acids 19 to 397 of SEQ ID NO: 2 comprising asubstitution, deletion, and/or insertion at one or several positions;and

(e) a fragment of the catalytic domain of (a), (b), (c), or (d) that hasendoglucanase activity.

Embodiment 8

The polypeptide of embodiment 7, further comprising a cellulose bindingdomain.

Embodiment 9

An isolated polypeptide comprising a cellulose binding domain operablylinked to a catalytic domain, wherein the binding domain is selectedfrom the group consisting of:

(a) a cellulose binding domain having at least 80% sequence identity toamino acids 444 to 477 of SEQ ID NO: 2;

(b) a cellulose binding domain encoded by a polynucleotide thathybridizes under high, or very high stringency conditions with (i)nucleotides 1333 to 1431 of SEQ ID NO: 1, or (ii) the full-lengthcomplement of (i);

(c) a cellulose binding domain encoded by a polynucleotide having atleast 80% sequence identity to nucleotides 1333 to 1431 of SEQ ID NO: 1;

(d) a variant of amino acids 444 to 477 of SEQ ID NO: 2 comprising asubstitution, deletion, and/or insertion at one or several positions;and

(e) a fragment of (a), (b), (c), (d) or (e) that has cellulose bindingactivity.

Embodiment 10

The polypeptide of embodiment 9, wherein the catalytic domain isobtained from a hydrolase, isomerase, ligase, lyase, oxidoreductase, ortransferase, e.g., an aminopeptidase, amylase, carbohydrase,carboxypeptidase, catalase, cellobiohydrolase, cellulase, chitinase,cutinase, cyclodextrin glycosyltransferase, deoxyribonuclease,endoglucanase, esterase, alpha-galactosidase, beta-galactosidase,glucoamylase, alpha-glucosidase, beta-glucosidase, invertase, laccase,lipase, mannosidase, mutanase, oxidase, pectinolytic enzyme, peroxidase,phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease,transglutaminase, xylanase, or beta-xylosidase.

Embodiment 11

A composition comprising the polypeptide of any of embodiments 1-10.

Embodiment 12

The composition of embodiment 11, further comprising acellobiohydrolase, and a beta-glucosidase.

Embodiment 13

A method for degrading or converting a cellulosic material, comprising:treating the cellulosic material with an enzyme composition in thepresence of the polypeptide having endoglucanase activity of any ofembodiments 1-8.

Embodiment 14

The method of embodiment 13, wherein the cellulosic material ispretreated.

Embodiment 15

The method of embodiment 13 or 14, wherein the enzyme compositioncomprises one or more enzymes selected from the group consisting of acellulase, a polypeptide having cellulolytic enhancing activity, ahemicellulase, an esterase, a protease, a laccase, or a peroxidase.

Embodiment 16

The method of embodiment 15, wherein the cellulase is one or moreenzymes selected from the group consisting of an endoglucanase, acellobiohydrolase, and a beta-glucosidase.

Embodiment 17

The method of embodiment 15, wherein the hemicellulase is one or moreenzymes selected from the group consisting of a xylanase, an acetyxylanesterase, a feruloyl esterase, an arabinofuranosidase, a xylosidase, anda glucuronidase.

Embodiment 18

The method of any of embodiments 13-17, further comprising recoveringthe degraded cellulosic material.

Embodiment 19

The method of embodiment 18, wherein the degraded cellulosic material isa sugar.

Embodiment 20

The method of embodiment 19, wherein the sugar is selected from thegroup consisting of glucose, xylose, mannose, galactose, and arabinose.

Embodiment 21

A method for producing a fermentation product, comprising:

(a) saccharifying a cellulosic material with an enzyme composition inthe presence of the polypeptide having endoglucanase activity of any ofembodiments 1-8;

(b) fermenting the saccharified cellulosic material with one or morefermenting microorganisms to produce the fermentation product; and

(c) recovering the fermentation product from the fermentation.

Embodiment 22

The method of embodiment 21, wherein the cellulosic material ispretreated.

Embodiment 23

The method of embodiment 21 or 22, wherein the enzyme compositioncomprises one or more enzymes selected from the group consisting of acellulase, a polypeptide having cellulolytic enhancing activity, ahemicellulase, an esterase, a protease, a laccase, or a peroxidase.

Embodiment 24

The method of embodiment 23, wherein the cellulase is one or moreenzymes selected from the group consisting of an endoglucanase, acellobiohydrolase, and a beta-glucosidase.

Embodiment 25

The method of embodiment 23, wherein the hemicellulase is one or moreenzymes selected from the group consisting of a xylanase, an acetyxylanesterase, a feruloyl esterase, an arabinofuranosidase, a xylosidase, anda glucuronidase.

Embodiment 26

The method of any of embodiments 21-25, wherein steps (a) and (b) areperformed simultaneously in a simultaneous saccharification andfermentation.

Embodiment 27

The method of any of embodiments 21-26, wherein the fermentation productis an alcohol, an organic acid, a ketone, an amino acid, or a gas.

Embodiment 28

A method of fermenting a cellulosic material, comprising: fermenting thecellulosic material with one or more fermenting microorganisms, whereinthe cellulosic material is saccharified with an enzyme composition inthe presence of a polypeptide having endoglucanase activity of any ofembodiments 1-8.

Embodiment 29

The method of embodiment 28, wherein the fermenting of the cellulosicmaterial produces a fermentation product.

Embodiment 30

The method of embodiment 29, further comprising recovering thefermentation product from the fermentation.

Embodiment 31

The method of any of embodiments 28-30, wherein the cellulosic materialis pretreated before saccharification.

Embodiment 32

The method of any of embodiments 28-31, wherein the enzyme compositioncomprises one or more enzymes selected from the group consisting of acellulase, a polypeptide having cellulolytic enhancing activity, ahemicellulase, an esterase, a protease, a laccase, or a peroxidase.

Embodiment 33

The method of embodiment 32, wherein the cellulase is one or moreenzymes selected from the group consisting of an endoglucanase, acellobiohydrolase, and a beta-glucosidase.

Embodiment 34

The method of embodiment 32, wherein the hemicellulase is one or moreenzymes selected from the group consisting of a xylanase, an acetyxylanesterase, a feruloyl esterase, an arabinofuranosidase, a xylosidase, anda glucuronidase.

Embodiment 35

The method of any of embodiments 29-34, wherein the fermentation productis an alcohol, an organic acid, a ketone, an amino acid, or a gas.

Embodiment 36

An isolated polynucleotide encoding the polypeptide of any ofembodiments 1-10.

Embodiment 37

A nucleic acid construct or expression vector comprising thepolynucleotide of embodiment 36 operably linked to one or more controlsequences that direct the production of the polypeptide in an expressionhost.

Embodiment 38

A recombinant host cell comprising the polynucleotide of embodiment 36operably linked to one or more control sequences that direct theproduction of the polypeptide.

Embodiment 39

A method of producing the polypeptide of any of embodiments 1-10,comprising:

(a) cultivating a cell, which in its wild-type form produces thepolypeptide, under conditions conducive for production of thepolypeptide; and

(b) recovering the polypeptide.

Embodiment 40

A method of producing a polypeptide having endoglucanase activity,comprising:

(a) cultivating the host cell of embodiment 38 under conditionsconducive for production of the polypeptide; and

(b) recovering the polypeptide.

Embodiment 41

A transgenic plant, plant part or plant cell transformed with apolynucleotide encoding the polypeptide of any of embodiments 1-10.

Embodiment 42

A method of producing a polypeptide having endoglucanase activity,comprising:

(a) cultivating the transgenic plant or plant cell of embodiment 41under conditions conducive for production of the polypeptide; and

(b) recovering the polypeptide.

Embodiment 43

An isolated signal peptide comprising or consisting of amino acids 1 to18 of SEQ ID NO: 2.

Embodiment 44

An isolated polynucleotide encoding a signal peptide comprising orconsisting of amino acids 1 to 18 of SEQ ID NO: 2.

Embodiment 45

A nucleic acid construct or expression vector comprising a gene encodinga protein operably linked to the polynucleotide of embodiment 44,wherein the gene is foreign to the polynucleotide encoding the signalpeptide.

Embodiment 46

A recombinant host cell comprising a gene encoding a protein operablylinked to the polynucleotide of embodiment 44, wherein the gene isforeign to the polynucleotide encoding the signal peptide.

Embodiment 47

A method of producing a protein, comprising:

(a) cultivating a recombinant host cell comprising a gene encoding aprotein operably linked to the polynucleotide of embodiment 44, whereinthe gene is foreign to the polynucleotide encoding the signal peptide,under conditions conducive for production of the protein; and

(b) recovering the protein.

EXAMPLES Materials

Chemicals used as buffers and substrates were commercial products of atleast reagent grade.

Strains

Talaromyces leycettanus Strain CBS398.68 was used as the source of apolypeptide having endoglucanase activity. Aspergillus oryzae MT3568strain was used for expression of the Talaromyces leycettanus geneencoding the polypeptide having endoglucanase activity. A. oryzae MT3568is an amdS (acetamidase) disrupted gene derivative of Aspergillus oryzaeJaL355 (WO 2002/40694) in which pyrG auxotrophy was restored bydisrupting the A. oryzae acetamidase (amdS) gene.

Media and Solutions

YP+2% glucose medium was composed of 1% yeast extract, 2% peptone and 2%glucose.

PDA agar plates were composed of potato infusion (potato infusion wasmade by boiling 300 g of sliced (washed but unpeeled) potatoes in waterfor 30 minutes and then decanting or straining the broth throughcheesecloth. Distilled water was then added until the total volume ofthe suspension was one liter, followed by 20 g of dextrose and 20 g ofagar powder. The medium was sterilized by autoclaving at 15 psi for 15minutes (Bacteriological Analytical Manual, 8th Edition, Revision A,1998).

LB plates were composed of 10 g of Bacto-Tryptone, 5 g of yeast extract,10 g of sodium chloride, 15 g of Bacto-agar, and deionized water to 1liter. The medium was sterilized by autoclaving at 15 psi for 15 minutes(Bacteriological Analytical Manual, 8th Edition, Revision A, 1998).

COVE sucrose plates were composed of 342 g Sucrose (Sigma S-9378), 20 gAgar powder, 20 ml Cove salt solution (26 g MgSO₄.7H₂O, 26 g KCL, 26 gKH₂PO₄, 50 ml Cove trace metal solution) and deionized water to 1liter), and deionized water to 1 liter). The medium was sterilized byautoclaving at 15 psi for 15 minutes (Bacteriological Analytical Manual,8th Edition, Revision A, 1998). The medium was cooled to 60° C. andadded 10 mM acetamide, 15 mM CsCl, Triton X-100 (50 μl/500 ml)).

Cove trace metal solution was composed of 0.04 g Na₂B₄O₇.10H₂O, 0.4 gCuSO₄.5H₂O, 1.2 g FeSO₄.7H₂O, 0.7 g MnSO₄.H₂O, 0.8 g Na₂MoO₄.2H₂O, 10 gZnSO₄.7H₂O, and deionized water to 1 liter.

Dap-4C medium was composed of 20 g Dextrose, 10 g Maltose, 11 gMgSO₄.7H₂O, 1 g KH₂PO₄, 2 g Citric Acid, 5.2 g K₃PO₄.H₂O, 0.5 g YeastExtract (Difco), 1 ml Dowfax 63N10 (Dow Chemical Company), 0.5 ml KU6trace metals solution, 2.5 g CaCO₃, and deionized water to 1 liter. Themedium was sterilized by autoclaving at 15 psi for 15 minutes(Bacteriological Analytical Manual, 8th Edition, Revision A, 1998).Before use, Dap-4C medium was added 3.5 ml sterile 50% (NH₄)₂HPO₄ and 5ml sterile 20% Lactic Acid per 150 ml medium.

KU6 trace metals solution was composed of 0.13 g NiCl₂, 2.5 gCuSO₄.5H₂O, 13.9 g FeSO₄.7H₂O, 8.45 g MnSO₄.H₂O, 6.8 g ZnCl₂, 3 g CitricAcid, and deionized water to 1 liter.

Example 1 Source of DNA Sequence Information for Talaromyces leycettanusStrain CBS398.68

Genomic sequence information was generated by Illumina DNA sequencing atthe Beijing Genome Institute (BGI) in Beijing, China from genomic DNAisolated from Talaromyces leycettanus Strain CBS398.68. A preliminaryassembly of the genome was analyzed using the Pedant-Pro™ SequenceAnalysis Suite (Biomax Informatics AG, Martinsried, Germany). Genemodels constructed by the software were used as a starting point fordetecting GH7 homologues in the genome. More precise gene models wereconstructed manually using multiple known GH7 protein sequences as aguide.

Example 2 Talaromyces Leycettanus Strain CBS398.68 Genomic DNAExtraction

To generate genomic DNA for PCR amplification, Talaromyces leycettanusStrain CBS398.68 was propagated on PDA agar plates by growing at 26° C.for 7 days. Spores harvested from the PDA plates were used to inoculate25 ml of YP+2% glucose medium in a baffled shake flask and incubated at30° C. for 72 hours with agitation at 85 rpm.

Genomic DNA was isolated according to a modified DNeasy Plant Maxi kitprotocol (Qiagen Danmark, Copenhagen, Denmark). The fungal material fromthe above culture was harvested by centrifugation at 14,000×g for 2minutes. The supernatant was removed and the 0.5 g of the pellet wasfrozen in liquid nitrogen with quartz sand and grinded to a fine powderin a pre-chilled mortar. The powder was transferred to a 15 mlcentrifuge tube and added 5 ml buffer AP1 (preheated to 65° C.) and 10μl RNase A stock solution (100 mg/ml) followed by vigorous vortexing.After incubation for 10 minutes at 65° C. with regular inverting of thetube, 1.8 ml buffer AP2 was added to the lysate by gentle mixingfollowed by incubation on ice for 10 min. The lysate was thencentrifugated at 3000×g for 5 minutes at room temperature and thesupernatant was decanted into a QiAshredder maxi spin column placed in a50 ml collection tube. This was followed by centrifugation at 3000×g for5 minutes at room temperature. The flow-through was transferred into anew 50 ml tube and added 1.5 volumes of buffer AP3/E followed byvortexing. 15 ml of the sample was transferred into a DNeasy Maxi spincolumn placed in a 50 ml collection tube and centrifuged at 3000×g for 5minutes at room temperature. The flow-through was discarded and 12 mlbuffer AW was added to the DNeasy Maxi spin column placed in a 50 mlcollection tube and centrifuged at 3000×g for 10 minutes at roomtemperature. After discarding the flow-through, centrifugation wasrepeated to dispose of the remaining alcohol. The DNeasy Maxi spincolumn was transferred to a new 50 ml tube and 0.5 ml buffer AE(preheated to 70° C.) was added. After incubation for 5 minutes at roomtemperature, the sample was eluded by centrifugation at 3000×g for 5minutes at room temperature. Elution was repeated with an additional 0.5ml buffer AE and the eluates were combined. The concentration of theharvested DNA was measured by a UV spectrophotometer at 260 nm.

Example 3 Construction of an Aspergillus oryzae Expression VectorContaining Talaromyces Leycettanus Strain CBS398.68 Genomic SequenceEncoding a Family GH7 Polypeptide Having Endoglucanase Activity

Two synthetic oligonucleotide primers shown below were designed to PCRamplify the Talaromyces leycettanus Strain CBS398.68 P23YSZ gene fromthe genomic DNA prepared in Example 2. An IN-FUSION™ Cloning Kit (BDBiosciences, Palo Alto, Calif., USA) was used to clone the fragmentdirectly into the expression vector pDau109 (WO 2005/042735).

F-P23YSZ (SEQ ID NO: 3) 5′-ACACAACTGGGGATCCACCATGGCTCCAAAACTCGCT-3′R-P23YSZ (SEQ ID NO: 4) 5′-CCCTCTAGATCTCGAG CGCCTCCAACATTGTCGATT-3′Bold letters represent gene sequence. The underlined sequence ishomologous to the insertion sites of pDau 109.

An MJ Research PTC-200 DNA engine was used to perform the PCR reaction.A Phusion® High-Fidelity PCR Kit (Finnzymes Oy, Espoo, Finland) was usedfor the PCR amplification. The PCR reaction was composed of 5 μl of 5×HFbuffer (Finnzymes Oy, Espoo, Finland), 0.5 μl of dNTPs (10 mM), 0.5 μlof Phusion® DNA polymerase (0.2 units/μl) (Finnzymes Oy, Espoo,Finland), 1 μl of primer F—P23YSZ (5 μM), 1 μl of primer R—P23YSZ (5μM), 0.5 μl of Talaromyces leycettanus genomic DNA (100 ng/μl), and 16.5μl of deionized water in a total volume of 25 μl. The PCR conditionswere 1 cycle at 95° C. for 2 minutes. 35 cycles each at 98° C. for 10seconds, 60° C. for 30 seconds, and 72° C. for 2 minutes; and 1 cycle at72° C. for 10 minutes. The sample was then held at 12° C. until removedfrom the PCR machine.

The reaction products were isolated by 1.0% agarose gel electrophoresisusing 40 mM Tris base, 20 mM sodium acetate, 1 mM disodium EDTA (TAE)buffer where a 1513 bp product band was excised from the gel andpurified using an illustra GFX® PCR DNA and Gel Band Purification Kit(GE Healthcare Life Sciences, Brondby, Denmark) according to themanufacturer's instructions. The fragment was then cloned into Barn HIand Xho I digested pDau109 using an IN-FUSION™ Cloning Kit resulting inplasmid pP23YSZ. Cloning of the P23YSZ gene into Barn HI-Xho I digestedpDau109 resulted in the transcription of the Talaromyces leycettanusP23YSZ gene under the control of a NA2-tpi double promoter. NA2-tpi is amodified promoter from the gene encoding the Aspergillus niger neutralalpha-amylase in which the untranslated leader has been replaced by anuntranslated leader from the gene encoding the Aspergillus nidulanstriose phosphate isomerase.

The cloning protocol was performed according to the IN-FUSION™ CloningKit instructions generating a P23YSZ GH7 construct. The treated plasmidand insert were transformed into One Shot® TOP10F″ Chemically CompetentE. coli cells (Invitrogen, Carlsbad, Calif., USA) according to themanufacturer's protocol and plated onto LB plates supplemented with 0.1mg of ampicillin per ml. After incubating at 37° C. overnight, colonieswere seen growing under selection on the LB ampicillin plates. Fourcolonies transformed with the P23YSZ GH7 construct were cultivated in LBmedium supplemented with 0.1 mg of ampicillin per ml and plasmid wasisolated with a QIAprep Spin Miniprep Kit (QIAGEN Inc., Valencia,Calif., USA) according to the manufacturer's protocol.

Isolated plasmids were sequenced with vector primers and P23YSZ genespecific primers in order to determine a representative plasmidexpression clone that was free of PCR errors.

Example 4 Characterization of the Talaromyces leycettanus CBS398.68Genomic Sequence Encoding a P23YSZ GH7 Polypeptide Having EndoglucanaseActivity

DNA sequencing of the Talaromyces leycettanus CBS398.68 P23YSZ GH7genomic clone was performed with an Applied Biosystems Model 3700Automated DNA Sequencer using version 3.1 BIG-DYE™ terminator chemistry(Applied Biosystems, Inc., Foster City, Calif., USA) and primer walkingstrategy. Nucleotide sequence data were scrutinized for quality and allsequences were compared to each other with assistance of PHRED/PHRAPsoftware (University of Washington, Seattle, Wash., USA). The sequenceobtained was identical to the sequence from the BGI.

The nucleotide sequence and deduced amino acid sequence of theTalaromyces leycettanus P23YSZ gene is shown in SEQ ID NO: 1 and SEQ IDNO: 2, respectively. The coding sequence is 1434 bp including the stopcodon. The encoded predicted protein is 477 amino acids. Using theSignalP program (Nielsen et al., 1997, Protein Engineering 10:1-6), asignal peptide of 18 residues was predicted. The predicted matureprotein contains 459 amino acids with a predicted molecular mass of 48kDa and an isoelectric pH of 4.16.

A comparative pairwise global alignment of amino acid sequences wasdetermined using the Needleman and Wunsch algorithm (Needleman andWunsch, 1970, J. Mol. Biol. 48: 443-453) with gap open penalty of 10,gap extension penalty of 0.5, and the EBLOSUM62 matrix. The alignmentshowed that the deduced amino acid sequence of the Talaromycesleycettanus gene encoding the P23YSZ GH7 polypeptide havingendoglucanase activity shares 74.2% identity (excluding gaps) to thededuced amino acid sequence of a predicted GH7 family protein fromNeosartorya fischeri (accession number SWISSPROT:A1 DKY9) withendoglucanase activity.

Example 5 Expression of the Talaromyces leycettanus GH7 EndoglucanaseP23YSZ

The expression plasmid pP23YSZ was transformed into Aspergillus oryzaeMT3568. Aspergillus oryzae MT3568 is an AMDS (acetamidase) disruptedderivative of JaL355 (WO 2002/40694) in which pyrG auxotrophy wasrestored in the process of knocking out the A, oryzae acetamidase (AMDS)gene. MT3568 protoplasts are prepared according to the method ofEuropean Patent, EP0238023, pages 14-15, which are incorporated hereinby reference.

Transformants were purified on COVE sucrose selection plates throughsingle conidia prior to sporulating them on PDA plates. Production ofthe Talaromyces leycettanus GH7 polypeptide by the transformants wasanalyzed from culture supernatants of 1 ml 96 deep well stationarycultivations at 30° C. in YP+2% glucose medium. Expression was verifiedon an E-Page 8% SDS-PAGE 48 well gel (Invitrogen, Carlsbad, Calif., USA)by Coomassie staining. One transformant was selected for further workand designated Aspergillus oryzae 90.3.

For larger scale production, Aspergillus oryzae 90.3 spores were spreadonto a PDA plate and incubated for five days at 37° C. The confluentspore plate was washed twice with 5 ml of 0.01% TWEEN® 20 to maximizethe number of spores collected. The spore suspension was then used toinoculate twenty five 500 ml flasks containing 100 ml of Dap-4C medium.The culture was incubated at 30° C. with constant shaking at 100 rpm. Atday four post-inoculation, the culture broth was collected by filtrationthrough a bottle top MF75 Supor MachV 0.2 μm PES filter (Therm FisherScientific, Roskilde, Denmark). Fresh culture broth from thistransformant produced a band of GH7 protein of approximately 70 kDa. Theidentity of this band as the Talaromyces leycettanus GH7 polypeptide wasverified by peptide sequencing.

Example 6 Alternative Method for Producing the Talaromyces leycettanusGH7 Endoglucanase P23YSZ

Based on the nucleotide sequence identified as SEQ ID NO: 1, a syntheticgene can be obtained from a number of vendors such as Gene Art (GENEARTAG BioPark, Josef-Engert-Str. 11, 93053, Regensburg, Germany) or DNA 2.0(DNA2.0, 1430 O'Brien Drive, Suite E, Menlo Park, Calif. 94025, USA).The synthetic gene can be designed to incorporate additional DNAsequences such as restriction sites or homologous recombination regionsto facilitate cloning into an expression vector.

Using the two synthetic oligonucleotide primers F—P23YSZ and F—P23YSZdescribed above, a simple PCR reaction can be used to amplify thefull-length open reading frame from the synthetic gene of SEQ ID NO: 1.The gene can then be cloned into an expression vector for example asdescribed above and expressed in a host cell, for example in Aspergillusoryzae as described above.

Example 7 Purification of the Talaromyces leycettanus GH7 EndoglucanaseP23YSZ

1000 ml broth of the Aspergillus oryzae expression strain 90.3 wasadjusted to pH 7.0 and filtrated on 0.22 μm PES filter (Thermo FisherScientific, Roskilde, Denmark). Following, the filtrate was added 1.8 Mammonium sulphate. The filtrate was loaded onto a Phenyl Sepharose™ 6Fast Flow column (high sub) (GE Healthcare, Piscataway, N.J., USA)(column volume 60 mL) equilibrated with 1.8 M ammonium sulphate pH 7.0,25 mM HEPES pH7.0. After application the column was washed with 3 columnvolumes of 1.0 M ammonium sulphate and the protein eluted following with5 column volumes of 25 mM HEPES pH 7.0 at a flow rate of 15 ml/min.Fractions of 10 mL were collected and analyzed by SDS-page. Thefractions were pooled and applied to a Sephadex™ G-25 (medium) (GEHealthcare, Piscataway, N.J., USA) column equilibrated in 25 mM HEPES pH7.0. The fractions were applied to a SOURCE™ 15Q (GE Healthcare,Piscataway, N.J., USA) column equilibrated in 25 mM HEPES pH 7.0 (columnvolume 60 mL). After application the column was washed with 3 columnvolumes equilibration buffer and bound proteins were eluted with alinear gradient over 20 column volumes from 0-500 mM sodium chloride.Fractions of 10 ml were collected and analyzed by SDS-page, andfractions with the protein were pooled to a final volume of 148 ml. Theprotein concentration was determined by A280/A260 absorbance.

Example 8 Endoglucanase Assay

The concentrate is assayed for endoglucanase activity by a microtiterplate assay as described below. A solution of 0.2% AZCL-HE-Cellulose(Megazyme International Ireland, Ltd., Bray, Co. Wicklow, Ireland) ismade in a 0.1 M sodium acetate pH 5.5 buffer with stirring. The solutionis distributed under stirring to a microtiter plate (200 μl to eachwell). Then 20 μl of enzyme sample is added and incubated in anEPPENDORF® THERMOMIXER® (Eppendorf AG, Hamburg, Germany) for 20 minutesat 50° C. and 650 rpm. A denatured enzyme sample (100° C. boiling for 20minutes) is used as blank. After incubation the colored solution isseparated from the solid substrate by centrifugation at 3000 rpm for 5minutes at 4° C. A 150 μl sample of supernatant is transferred to amicrotiter plate; and the absorbance is measured at 595 nm using aSPECTRAMAX® M2 Multi-Mode Microplate Reader (Molecular Devices, Beijing,China).

Example 9 Pretreated Corn Stover Hydrolysis Assay

Corn stover was pretreated at the U.S. Department of Energy NationalRenewable Energy Laboratory (NREL) using 1.4 wt % sulfuric acid at 165°C. and 107 psi for 8 minutes. The water-insoluble solids in thepretreated corn stover (PCS) contained 56.5% cellulose, 4.6%hemicellulose and 28.4% lignin. Cellulose and hemicellulose weredetermined by a two-stage sulfuric acid hydrolysis with subsequentanalysis of sugars by high performance liquid chromatography using NRELStandard Analytical Procedure #002. Lignin was determinedgravimetrically after hydrolyzing the cellulose and hemicellulosefractions with sulfuric acid using NREL Standard Analytical Procedure#003.

Unmilled, unwashed PCS (whole slurry PCS) was prepared by adjusting thepH of PCS to 5.0 by addition of 10 M NaOH with extensive mixing, andthen autoclaving for 20 minutes at 120° C. The dry weight of the wholeslurry PCS was 29%. The PCS was used unwashed or washed with water.Milled unwashed PCS (dry weight 32.35%) was prepared by milling wholeslurry PCS in a Cosmos ICMG 40 wet multi-utility grinder (EssEmmCorporation, Tamil Nadu, India). Milled washed PCS (dry weight 32.35%)was prepared in the same manner, with subsequent washing with deionizedwater and decanting off the supernatant fraction repeatedly.

The hydrolysis of PCS was conducted using 2.2 ml deep-well plates(Axygen, Union City, Calif., USA) in a total reaction volume of 1.0 ml.The hydrolysis was performed with 50 mg of insoluble PCS solids per mlof 50 mM sodium acetate pH 5.0 buffer containing 1 mM manganese sulfateand various protein loadings of various enzyme compositions (expressedas mg protein per gram of cellulose). Enzyme compositions were preparedand then added simultaneously to all wells in a volume ranging from 50μl to 200 μl, for a final volume of 1 ml in each reaction. The plate wasthen sealed using an ALPS-300™ plate heat sealer (Abgene, Epsom, UnitedKingdom), mixed thoroughly, and incubated at a specific temperature for72 hours. All experiments reported were performed in triplicate.

Following hydrolysis, samples were filtered using a 0.45 μm MULTISCREEN®96-well filter plate (Millipore, Bedford, Mass., USA) and filtratesanalyzed for sugar content as described below. When not usedimmediately, filtered aliquots were frozen at −20° C. The sugarconcentrations of samples diluted in 0.005 M H₂₅O₄ were measured using a4.6×250 mm AMINEX® HPX-87H column (Bio-Rad Laboratories, Inc., Hercules,Calif., USA) by elution with 0.05% w/w benzoic acid-0.005 M H₂SO₄ at 65°C. at a flow rate of 0.6 ml per minute, and quantitation by integrationof the glucose, cellobiose, and xylose signals from refractive indexdetection (CHEMSTATION®, AGILENT® 1100 HPLC, Agilent Technologies, SantaClara, Calif., USA) calibrated by pure sugar samples. The resultantglucose and cellobiose equivalents were used to calculate the percentageof cellulose conversion for each reaction.

Glucose, cellobiose, and xylose were measured individually. Measuredsugar concentrations were adjusted for the appropriate dilution factor.The net concentrations of enzymatically-produced sugars from unwashedPCS were determined by adjusting the measured sugar concentrations forcorresponding background sugar concentrations in unwashed PCS at zerotime point. All HPLC data processing was performed using MICROSOFTEXCEL™ software (Microsoft, Richland, Wash., USA).

The degree of cellulose conversion to glucose was calculated using thefollowing equation: % conversion=(glucose concentration/glucoseconcentration in a limit digest)×100. In order to calculate %conversion, a 100% conversion point was set based on a cellulase control(100 mg of Trichoderma reesei cellulase per gram cellulose), and allvalues were divided by this number and then multiplied by 100.Triplicate data points were averaged and standard deviation wascalculated.

Example 10 Preparation of an Enzyme Composition

The Aspergillus fumigatus GH7A cellobiohydrolase I (SEQ ID NO: 5 [DNAsequence] and SEQ ID NO: 6 [deduced amino acid sequence]) was preparedrecombinantly in Aspergillus oryzae as described in WO 2011/057140. Thefiltered broth of Aspergillus fumigatus GH7A cellobiohydrolase I wasconcentrated and buffer exchanged using a tangential flow concentrator(Pall Filtron, Northborough, Mass., USA) equipped with a 10 kDapolyethersulfone membrane (Pall Filtron, Northborough, Mass., USA) with20 mM Tris-HCl pH 8.0. The desalted broth of Aspergillus fumigatus GH7Acellobiohydrolase I was purified over a Q SEPHAROSE™ ion exchangechromatography column (GE Healthcare, Piscataway, N.J., USA) in 20 mMTris-HCl pH 8, over a linear 0 to 1 M NaCl gradient. Fractions werecollected and fractions containing the cellobiohydrolase I cellulasewere pooled based on 8-16% CRITERION® Stain-free SDS-PAGE (Bio-RadLaboratories, Inc., Hercules, Calif., USA).

Preparation of Aspergillus fumigatus NN055679 cellobiohydrolase II. TheAspergillus fumigatus GH6A cellobiohydrolase II (SEQ ID NO: 7 [DNAsequence] and SEQ ID NO: 8 [deduced amino acid sequence]) was preparedrecombinantly in Aspergillus oryzae as described in WO 2011/057140. Thefiltered broth of Aspergillus fumigatus GH6A cellobiohydrolase II wasbuffer exchanged into 20 mM Tris pH 8.0 using a 400 ml SEPHADEX™ G-25column (GE Healthcare, United Kingdom) according to the manufacturer'sinstructions. The fractions were pooled and adjusted to 1.2 M ammoniumsulphate-20 mM Tris pH 8.0. The equilibrated protein was loaded onto aPHENYL SEPHAROSE™ 6 Fast Flow column (high sub) (GE Healthcare,Piscataway, N.J., USA) equilibrated in 20 mM Tris pH 8.0 with 1.2 Mammonium sulphate, and bound proteins were eluted with 20 mM Tris pH 8.0with no ammonium sulphate. The fractions were pooled.

Preparation of Penicillium sp. (emersonii) GH61A polypeptide havingcellulolytic enhancing activity. The Penicillium sp. (emersonii) GH61Apolypeptide (SEQ ID NO: 9 [DNA sequence] and SEQ ID NO: 10 [deducedamino acid sequence]) was recombinantly prepared according to WO2011/041397. The Penicillium sp. (emersonii) GH61A polypeptide gene waspurified according to WO 2011/041397.

Preparation of Aspergillus fumigatus NN055679 GH10 xylanase. TheAspergillus fumigatus GH10 xylanase (xyn3) (SEQ ID NO: 11 [DNA sequence]and SEQ ID NO: 12 [deduced amino acid sequence]) was preparedrecombinantly according to WO 2006/078256 using Aspergillus oryzae BECh2(WO 2000/39322) as a host. The filtered broth of Aspergillus fumigatusNN055679 GH10 xylanase (xyn3) was desalted and buffer-exchanged into 50mM sodium acetate pH 5.0 using a HIPREP® 26/10 Desalting Column (GEHealthcare, Piscataway, N.J., USA) according to the manufacturer'sinstructions.

Preparation of Aspergillus fumigatus NN055679 Cel3A beta-glucosidase.(SEQ ID NO: 13 [DNA sequence] and SEQ ID NO: 14 [deduced amino acidsequence]) was recombinantly prepared according to WO 2005/047499 usingAspergillus oryzae as a host. The filtered broth was adjusted to pH 8.0with 20% sodium acetate, which made the solution turbid. To remove theturbidity, the solution was centrifuged (20000×g, 20 minutes), and thesupernatant was filtered through a 0.2 μm filtration unit (Nalgene,Rochester, N.Y., USA). The filtrate was diluted with deionized water toreach the same conductivity as 50 mM Tris/HCl, pH 8.0. The adjustedenzyme solution was applied to a Q SEPHAROSE™ Fast Flow column (GEHealthcare, Piscataway, N.J., USA) equilibrated in 50 mM Tris-HCl, pH8.0 and eluted with a linear gradient from 0 to 500 mM sodium chloride.Fractions were pooled and treated with 1% (w/v) activated charcoal toremove color from the beta-glucosidase pool. The charcoal was removed byfiltration of the suspension through a 0.2 μm filtration unit (Nalgene,Rochester, N.Y., USA). The filtrate was adjusted to pH 5.0 with 20%acetic acid and diluted 10 times with deionized water. The adjustedfiltrate was applied to a SP SEPHAROSE™ Fast Flow column (GE Healthcare,Piscataway, N.J., USA) equilibrated in 10 mM succinic acid, pH 5.0 andeluted with a linear gradient from 0 to 500 mM sodium chloride.

Preparation of Aspergillus fumigatus NN051616 GH3 beta-xylosidase. TheAspergillus fumigatus GH3 beta-xylosidase (SEQ ID NO: 15 [DNA sequence]and SEQ ID NO: 16 [deduced amino acid sequence]) was preparedrecombinantly in Aspergillus oryzae as described in WO 2011/057140. Thefiltered broth of Aspergillus fumigatus NN051616 GH3 beta-xylosidase wasdesalted and buffer-exchanged into 50 mM sodium acetate pH 5.0 using aHIPREP® 26/10 Desalting Column (GE Healthcare, Piscataway, N.J., USA)according to the manufacturer's instructions.

The protein concentration for each of the monocomponents described abovewas determined using a Microplate BCA™ Protein Assay Kit (Thermo FischerScientific, Waltham, Mass., USA) in which bovine serum albumin was usedas a protein standard. An enzyme composition was composed of eachmonocomponent, prepared as described above, as follows: 37% Aspergillusfumigatus Cel7A cellobiohydrolase I, 25% Aspergillus fumigatus Cel6Acellobiohydrolase II, 15% Penicillium emersonii GH61A polypeptide havingcellulolytic enhancing activity, 5% Aspergillus fumigatus GH10 xylanase,5% Aspergillus fumigatus beta-glucosidase, and 3% Aspergillus fumigatusbeta-xylosidase. The enzyme composition is designated herein as “enzymecomposition without endoglucanase”.

Example 11 Preparation of Trichoderma reesei Endoglucanase II

Preparation of Trichoderma reesei GH5 endoglucanase II. The Trichodermareesei GH5 endoglucanase II (SEQ ID NO: 17 [DNA sequence] and SEQ ID NO:18 [deduced amino acid sequence]) was prepared recombinantly accordingto WO 2011/057140 using Aspergillus oryzae as a host. The filtered brothof Trichoderma reesei GH5 endoglucanase II was desalted andbuffer-exchanged into 20 mM Tris pH 8.0 using tangential flow (10Kmembrane, Pall Filtron, Northborough, Mass., USA) according to themanufacturer's instructions.

Example 12 Effect of Talaromyces leycettanus Family GH7 Endoglucanase I(P23YSZ) in the Hydrolysis of Milled Unwashed PCS at 50-65° C. By anEnzyme Composition

The Talaromyces leycettanus Family GH7 endoglucanase I (P23YSZ) wasevaluated in an enzyme composition without endoglucanase at 50° C., 55°C., 60° C., and 65° C. using milled unwashed PCS as a substrate. Theenzyme composition without endoglucanase (Example 10) was added to PCShydrolysis reactions at 2.7 mg total protein per g cellulose, and thehydrolysis results were compared with the results for a similar enzymecomposition with and without added GH7 endoglucanase (3.0 mg protein perg cellulose).

The assay was performed as described in Example 9. The 1 ml reactionswith milled unwashed PCS (5% insoluble solids) were conducted for 72hours in 50 mM sodium acetate pH 5.0 buffer containing 1 mM manganesesulfate. All reactions were performed in triplicate and involved singlemixing at the beginning of hydrolysis.

As shown in Table 1, below, the enzyme composition that included theTalaromyces leycettanus Family GH7 endoglucanase I (P23YSZ)significantly outperformed the enzyme composition without endoglucanase(2.7 mg protein/g cellulose and 3.0 mg protein/g cellulose) at 50° C.,55° C., 60° C., and 65° C. (as the degree of cellulose conversion toglucose for the Talaromyces leycettanus Family GH7 endoglucanase I(P23YSZ) was higher than the enzyme composition without endoglucanase at50° C., 55° C., 60° C., and 65° C.). The results in Table 1, below, showthat the enzyme composition that included Talaromyces leycettanus FamilyGH7 endoglucanase I (P23YSZ) performed about the same as the enzymecomposition that included Trichoderma reesei Family GH5 endoglucanase IIat 60° C. and 65° C. (as the degree of cellulose conversion to glucosefor Talaromyces leycettanus Family GH7 endoglucanase I (P23YSZ) wasabout the same as the enzyme composition containing Trichoderma reeseiFamily GH5 endoglucanase II at 60° C. and 65° C.).

TABLE 1 % Cellulose to Glucose Conversion Enzyme Composition 50° C. 55°C. 60° C. 65° C. Enzyme Composition w/o EG 32.02 34.92 31.81 26.49 (2.7mg/g) Enzyme Composition w/o EG 33.33 36.85 33.42 28.55 (3.0 mg/g)Enzyme Composition (2.7 mg/g) 56.06 58.49 45.99 37.94 with Trichodermareesei EGII (.3 mg/g) Enzyme Composition (2.7 mg/g) 51.40 53.59 45.1738.65 with Talaromyces leycettanus EGI (.3 mg/g)

Example 13 Evaluation of Two Endoglucanases on Milled Washed PCS at50-65° C.

Two endoglucanases were evaluated at 1 mg protein per g cellulose at 50°C., 55° C., 60° C., and 65° C. using milled washed PCS as a substratewith 1 mg protein per g cellulose of Aspergillus fumigatus Family GH3beta-glucosidase. The following endoglucanases were tested: Talaromycesleycettanus Family GH7 endoglucanase I (P23YSZ) and Trichoderma reeseiFamily GH5 endoglucanase II.

The assay was performed as described in Example 9. The 1 ml reactionswith milled washed PCS (5% insoluble solids) were conducted for 72 hoursin 50 mM sodium acetate pH 5.0 buffer containing 1 mM manganese sulfate.All reactions were performed in triplicate and involved single mixing atthe beginning of hydrolysis.

The results shown in Table 2, below, demonstrated that at 50° C., 55°C., 60° C., and 65° C. the Talaromyces leycettanus Family GH7endoglucanase I (P23YSZ) had higher cellulose to glucose conversion thanthat of the Trichoderma reesei Family GH5 endoglucanase II.

TABLE 2 % Cellulose to Glucose Conversion Enzyme Composition 50° C. 55°C. 60° C. 65° C. Trichoderma reesei EGII 3.91 4.01 4.14 3.51 (1 mg/g) +Aspergillus fumigatus bG (1 mg/g) Talaromyces leycettanus EGI 4.08 4.334.62 4.24 (1 mg/g) + Aspergillus fumigatus bG (1 mg/g)

The invention described and claimed herein is not to be limited in scopeby the specific aspects herein disclosed, since these aspects areintended as illustrations of several aspects of the invention. Anyequivalent aspects are intended to be within the scope of thisinvention. Indeed, various modifications of the invention in addition tothose shown and described herein will become apparent to those skilledin the art from the foregoing description. Such modifications are alsointended to fall within the scope of the appended claims. In the case ofconflict, the present disclosure including definitions will control.

1. An isolated polypeptide having endoglucanase activity, selected fromthe group consisting of: (a) a polypeptide having at least 75% sequenceidentity to the mature polypeptide of SEQ ID NO: 2; (b) a polypeptideencoded by a polynucleotide that hybridizes under medium-high stringencyconditions with (i) the mature polypeptide coding sequence of SEQ ID NO:1, or (ii) the full-length complement of (i); (c) a polypeptide encodedby a polynucleotide having at least 75% sequence identity to the maturepolypeptide coding sequence of SEQ ID NO: 1; (d) a variant of the maturepolypeptide of SEQ ID NO: 2 comprising a substitution, deletion, and/orinsertion at one or several positions; and (e) a fragment of thepolypeptide of (a), (b), (c), or (d) that has endoglucanase activity. 2.(canceled)
 3. The polypeptide of claim 1, comprising or consisting ofSEQ ID NO: 2 or the mature polypeptide of SEQ ID NO:
 2. 4. Thepolypeptide of claim 3, wherein the mature polypeptide is amino acids 19to 477 of SEQ ID NO:
 2. 5. An isolated polypeptide comprising acatalytic domain selected from the group consisting of: (a) a catalyticdomain having at least 80% sequence identity to amino acids 19 to 397 ofSEQ ID NO: 2; (b) a catalytic domain encoded by a polynucleotide thathybridizes under high, or very high stringency conditions with (i)nucleotides 55 to 1191 of SEQ ID NO: 1, or (ii) the full-lengthcomplement of (i); (c) a catalytic domain encoded by a polynucleotidehaving at least 80% sequence identity to the catalytic domain of SEQ IDNO: 1; (d) a variant of amino acids 19 to 397 of SEQ ID NO: 2 comprisinga substitution, deletion, and/or insertion at one or several positions;and (e) a fragment of the catalytic domain of (a), (b), (c), or (d) thathas endoglucanase activity.
 6. The polypeptide of claim 5, furthercomprising a cellulose binding domain.
 7. An isolated polypeptidecomprising a cellulose binding domain operably linked to a catalyticdomain, wherein the binding domain is selected from the group consistingof: (a) a cellulose binding domain having at least 80% sequence identityto amino acids 444 to 477 of SEQ ID NO: 2; (b) a cellulose bindingdomain encoded by a polynucleotide that hybridizes under high, or veryhigh stringency conditions with (i) nucleotides 1333 to 1431 of SEQ IDNO: 1, or (ii) the full-length complement of (i); (c) a cellulosebinding domain encoded by a polynucleotide having at least 80% sequenceidentity to nucleotides 1333 to 1431 of SEQ ID NO: 1; (d) a variant ofamino acids 444 to 477 of SEQ ID NO: 2 comprising a substitution,deletion, and/or insertion at one or several positions; and (e) afragment of (a), (b), (c), (d) or (e) that has cellulose bindingactivity.
 8. A composition comprising the polypeptide of claim
 1. 9. Amethod for degrading or converting a cellulosic material, comprising:treating the cellulosic material with an enzyme composition in thepresence of the polypeptide having endoglucanase activity of claim 1.10-12. (canceled)
 13. A method for producing a fermentation product,comprising: (a) saccharifying a cellulosic material with an enzymecomposition in the presence of the polypeptide having endoglucanaseactivity of claim 1; (b) fermenting the saccharified cellulosic materialwith one or more fermenting microorganisms to produce the fermentationproduct; and (c) recovering the fermentation product from thefermentation. 14-15. (canceled)
 16. A method of fermenting a cellulosicmaterial, comprising: fermenting the cellulosic material with one ormore fermenting microorganisms, wherein the cellulosic material issaccharified with an enzyme composition in the presence of a polypeptidehaving endoglucanase activity of claim
 1. 17. An isolated polynucleotideencoding the polypeptide of claim
 1. 18. A nucleic acid construct orexpression vector comprising the polynucleotide of claim 17 operablylinked to one or more control sequences that direct the production ofthe polypeptide in an expression host.
 19. A recombinant host cellcomprising the polynucleotide of claim 17 operably linked to one or morecontrol sequences that direct the production of the polypeptide.
 20. Amethod of producing a polypeptide having endoglucanase activity,comprising: (a) cultivating the host cell of claim 19 under conditionsconducive for production of the polypeptide; and (b) recovering thepolypeptide.
 21. An isolated polynucleotide encoding a signal peptidecomprising or consisting of amino acids 1 to 18 of SEQ ID NO:
 2. 22. Anucleic acid construct or expression vector comprising a gene encoding aprotein operably linked to the polynucleotide of claim 21, wherein thegene is foreign to the polynucleotide encoding the signal peptide.
 23. Arecombinant host cell comprising a gene encoding a protein operablylinked to the polynucleotide of claim 21, wherein the gene is foreign tothe polynucleotide encoding the signal peptide.
 24. A method ofproducing a protein, comprising: (a) cultivating a recombinant host cellcomprising a gene encoding a protein operably linked to thepolynucleotide of claim 21, wherein the gene is foreign to thepolynucleotide encoding the signal peptide, under conditions conducivefor production of the protein; and (b) recovering the protein.